Mercurial > repos > devteam > pgsnp2gd_snp
changeset 0:d281062566f9 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 28 Jul 2014 11:55:36 -0400 |
| parents | |
| children | 4cd611004dc4 |
| files | pgSnp2gd_snp.pl pgSnp2gd_snp.xml test-data/pgSnp2snp_output.txt test-data/pgSnpTest.ref.txt |
| diffstat | 4 files changed, 20307 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pgSnp2gd_snp.pl Mon Jul 28 11:55:36 2014 -0400 @@ -0,0 +1,208 @@ +#!/usr/bin/perl -w +use strict; + +#convert from pgSnp file to snp table (Webb format?) + +#snp table format: +#1. chr +#2. position (0 based) +#3. ref allele +#4. second allele +#5. overall quality +#foreach individual (6-9, 10-13, ...) +#a. count of allele in 3 +#b. count of allele in 4 +#c. genotype call (-1, or count of ref allele) +#d. quality of genotype call (quality of non-ref allele from masterVar) + +if (!@ARGV) { + print "usage: pgSnp2gd_snp.pl file.pgSnp[.gz|.bz2] [-tab=snpTable.txt -addColsOnly -build=hg19 -name=na -ref=#1based -chr=#1based ] > newSnpTable.txt\n"; + exit; +} + +my $in = shift @ARGV; +my $tab; +my $tabOnly; +my $build; +my $name; +my $ref; +my $binChr = 1; #position of chrom column, indicates if bin is added +foreach (@ARGV) { + if (/-tab=(.*)/) { $tab = $1; } + elsif (/-addColsOnly/) { $tabOnly = 1; } + elsif (/-build=(.*)/) { $build = $1; } + elsif (/-name=(.*)/) { $name = $1; } + elsif (/-ref=(\d+)/) { $ref = $1 - 1; } #go to index + elsif (/-chr=(\d+)/) { $binChr = $1; } +} + +if ($binChr == 2 && $ref) { $ref--; } #shift over by 1, we will delete bin +if ((!$tab or !$tabOnly) && !$ref) { + print "Error the reference allele must be in a column in the file if not just adding to a previous SNP table.\n"; + exit; +} + +#WARNING loads snp table in memory, this could take > 1G ram +my %old; +my $colcnt = 0; +my @head; +if ($tab) { + open(FH, $tab) or die "Couldn't open $tab, $!\n"; + while (<FH>) { + chomp; + if (/^#/) { push(@head, $_); next; } + my @f = split(/\t/); + $old{"$f[0]:$f[1]"} = join("\t", @f); + $colcnt = scalar @f; + } + close FH or die "Couldn't close $tab, $!\n"; +} + +if ($in =~ /.gz$/) { + open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; +}elsif ($in =~ /.bz2$/) { + open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n"; +}else { + open(FH, $in) or die "Couldn't open $in, $!\n"; +} +prepHeader(); +if (@head) { #keep old header, add new? + print join("\n", @head), "\n"; +} +while (<FH>) { + chomp; + if (/^#/) { next; } + if (/^\s*$/) { next; } + my @f = split(/\t/); + if ($binChr == 2) { #must have a bin column prepended on the beginning + shift @f; #delete it + } + if (!$f[3]) { next; } #WHAT? most likely still zipped? + if ($f[4] > 2) { next; } #can only do cases of 2 alleles + if ($f[2] == $f[1] or $f[2] - $f[1] != 1) { next; } #no indels + if ($f[3] =~ /-/) { next; } #no indels + #if creating a new table need the reference allele in a column + if (%old && $old{"$f[0]:$f[1]"}) { + my @o = split(/\t/, $old{"$f[0]:$f[1]"}); + my $freq = 0; + my $freq2 = 0; + my $sc; + my $g = 1; #genotype == ref allele count + if ($f[4] == 1) { #should be homozygous + if ($f[3] eq $o[2]) { $g = 2; $freq = $f[5]; } + elsif ($f[3] eq $o[3]) { $g = 0; $freq2 = $f[5]; } + else { next; } #doesn't match either allele, skip + $sc = $f[6]; + }else { + my $a = 0; #index of a alleles, freq, scores + my $b = 1; #same for b + my @all = split(/\//, $f[3]); + if ($o[2] ne $all[0] && $o[2] ne $all[1]) { next; } #must match one + if ($o[3] ne $all[0] && $o[3] ne $all[1]) { next; } + if ($o[2] eq $all[1]) { #switch indexes + $a = 1; + $b = 0; + } + my @fr = split(/,/, $f[5]); + $freq = $fr[$a]; + $freq2 = $fr[$b]; + my @s = split(/,/, $f[6]); + $sc = $s[$b]; + } + #print old + print $old{"$f[0]:$f[1]"}; + #add new columns + print "\t$freq\t$freq2\t$g\t$sc\n"; + $old{"$f[0]:$f[1]"} = ''; + }elsif (!$tabOnly) { #new table, or don't have this SNP + #need reference allele + if ($f[3] !~ /$f[$ref]/ && $f[4] == 2) { next; } #no reference allele + my $freq = 0; + my $freq2 = 0; + my $sc; + my $g = 1; #genotype == ref allele count + my $alt; + if ($f[4] == 1) { #should be homozygous + if ($f[3] eq $f[$ref]) { $g = 2; $freq = $f[5]; $alt = 'N'; } + else { $g = 0; $freq2 = $f[5]; $alt = $f[3]; } #matches alternate + $sc = $f[6]; + }else { + my $a = 0; #index of a alleles, freq, scores + my $b = 1; #same for b + my @all = split(/\//, $f[3]); + if ($f[$ref] ne $all[0] && $f[$ref] ne $all[1]) { next; } #must match one + if ($f[$ref] eq $all[1]) { #switch indexes + $a = 1; + $b = 0; + } + my @fr = split(/,/, $f[5]); + $freq = $fr[$a]; + $freq2 = $fr[$b]; + my @s = split(/,/, $f[6]); + $sc = $s[$b]; + $alt = $all[$b]; + } + #print initial columns + print "$f[0]\t$f[1]\t$f[$ref]\t$alt\t-1"; + #pad for other individuals if needed + my $i = 5; + while ($i < $colcnt) { + print "\t-1\t-1\t-1\t-1"; + $i += 4; + } + #add new columns + print "\t$freq\t$freq2\t$g\t$sc\n"; + } +} +close FH or die "Couldn't close $in, $!\n"; + +#if adding to a snp table, now we need to finish those not in the latest set +foreach my $k (keys %old) { + if ($old{$k} ne '') { #not printed yet + print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one + } +} + +exit; + +#parse old header and add or create new +sub prepHeader { + if (!$build) { $build = 'hg19'; } #set default + my @cnames; + my @ind; + my $n; + if (@head) { #parse previous header + my $h = join("", @head); #may split between lines + if ($h =~ /"column_names":\[(.*?)\]/) { + my @t = split(/,/, $1); + foreach (@t) { s/"//g; } + @cnames = @t; + $n = $cnames[$#cnames]; + $n =~ s/Q//; + $n++; + } + if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; } + if ($h =~ /"individuals":\[(.*)\]/) { + my $t = $1; + $t =~ s/\]\].*/]/; #remove if there is more categories + @ind = split(/,/, $t); + } + }else { #start new header + @cnames = ("chr", "pos", "A", "B", "Q"); + $n = 1; + } + #add current + if (!$name) { $name= 'na'; } + my $stcol = $colcnt + 1; + if ($stcol == 1) { $stcol = 6; } #move past initial columns + push(@ind, "[\"$name\",$stcol]"); + push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q"); + #reassign head + undef @head; + foreach (@cnames) { $_ = "\"$_\""; } #quote name + $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],"; + $head[1] = "#\"individuals\":[" . join(",", @ind) . "],"; + $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}"; +} +####End +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pgSnp2gd_snp.xml Mon Jul 28 11:55:36 2014 -0400 @@ -0,0 +1,97 @@ +<tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0"> + <description>Convert from pgSnp to gd_snp</description> + <command interpreter="perl"> + #if $snptab.tab2 == "yes" + #if $snptab.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=${ref} -chr=${input1.metadata.chromCol} > $out_file1 + #end if + #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1 + #end if + </command> + <inputs> + <param format="tab" 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 a gd_snp_ table. (`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 table or by backfilling), +then an extra column with the reference allele must be supplied in the pgSnp dataset, +as shown in the example below. + +----- + +**Example** + +- input pgSnp file, with reference allele added:: + + chr1 1888681 1888682 C/T 2 4,3 0.8893,0.8453 T + chr1 3118325 3118326 T 1 8 0.8796 C + chr1 3211457 3211458 A/C 2 17,10 0.8610,0.8576 A + etc. + +- gd_snp output:: + + chr1 1888681 T C -1 3 4 1 0.8893 + chr1 3118325 C T -1 0 8 0 0.8796 + chr1 3211457 A C -1 17 10 1 0.8576 + etc. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pgSnp2snp_output.txt Mon Jul 28 11:55:36 2014 -0400 @@ -0,0 +1,10002 @@ +#{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q"], +#"individuals":[["na",6]], +#"dbkey":"hg19","pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} +chr1 1888681 T C -1 3 4 1 0.8893 +chr1 3118325 C T -1 0 8 0 0.8796 +chr1 3211457 A C -1 17 10 1 0.8576 +chr1 3222692 G A -1 10 14 1 0.8694 +chr1 3281273 G A -1 5 4 1 0.8210 +chr1 3630475 C T -1 12 12 1 0.8430 +chr1 4599834 C T -1 0 18 0 0.8797 +chr1 5287107 T G -1 0 6 0 0.8443 +chr1 5307765 C T -1 22 12 1 0.8505 +chr1 5341621 A C -1 5 3 1 0.9001 +chr1 5478586 A G -1 0 11 0 0.8997 +chr1 5680961 A C -1 16 10 1 0.8135 +chr1 5736051 G A -1 34 57 1 0.8655 +chr1 5831207 C T -1 5 10 1 0.8575 +chr1 6200884 A C -1 0 13 0 0.8346 +chr1 6307254 T C -1 0 11 0 0.8723 +chr1 6621228 G T -1 10 11 1 0.8336 +chr1 7094424 G A -1 0 4 0 0.8578 +chr1 7392593 C T -1 15 25 1 0.8644 +chr1 7500089 C G -1 0 13 0 0.8508 +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 17498098 T C -1 0 3 0 0.7863 +chr1 17715847 G A -1 0 11 0 0.8438 +chr1 18857430 C T -1 17 14 1 0.8586 +chr1 19092742 G T -1 16 10 1 0.8678 +chr1 19525584 T C -1 0 12 0 0.8614 +chr1 19921477 C A -1 4 3 1 0.8781 +chr1 20044146 C T -1 5 6 1 0.8847 +chr1 20269168 T C -1 10 5 1 0.8936 +chr1 20947809 C T -1 0 8 0 0.8416 +chr1 21135182 C A -1 0 13 0 0.8384 +chr1 21941643 G T -1 0 12 0 0.8389 +chr1 22324976 C T -1 9 6 1 0.8158 +chr1 22708791 T A -1 12 8 1 0.8313 +chr1 22904350 A G -1 10 4 1 0.8523 +chr1 22928348 A G -1 0 7 0 0.8629 +chr1 23039691 G C -1 0 13 0 0.8484 +chr1 24392068 C T -1 0 4 0 0.8425 +chr1 24851230 A G -1 19 15 1 0.8807 +chr1 25158007 A G -1 7 12 1 0.8625 +chr1 25250192 C T -1 5 4 1 0.8827 +chr1 25349613 A G -1 0 6 0 0.8963 +chr1 25891773 C T -1 9 7 1 0.8869 +chr1 25989060 G A -1 5 14 1 0.8271 +chr1 25996483 A G -1 25 17 1 0.7880 +chr1 26172110 A G -1 24 13 1 0.8740 +chr1 26275739 T C -1 16 10 1 0.8335 +chr1 26436230 C A -1 14 18 1 0.8299 +chr1 27081694 G A -1 10 7 1 0.8297 +chr1 27215078 T C -1 5 9 1 0.8749 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pgSnpTest.ref.txt Mon Jul 28 11:55:36 2014 -0400 @@ -0,0 +1,10000 @@ +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 +chr1 3222692 3222693 A/G 2 14,10 0.8694,0.8619 G +chr1 3281273 3281274 A/G 2 4,5 0.8210,0.8427 G +chr1 3630475 3630476 C/T 2 12,12 0.8589,0.8430 C +chr1 4599834 4599835 T 1 18 0.8797 C +chr1 5287107 5287108 G 1 6 0.8443 T +chr1 5307765 5307766 C/T 2 22,12 0.8485,0.8505 C +chr1 5341621 5341622 A/C 2 5,3 0.8741,0.9001 A +chr1 5478586 5478587 G 1 11 0.8997 A +chr1 5680961 5680962 A/C 2 16,10 0.8671,0.8135 A +chr1 5736051 5736052 A/G 2 57,34 0.8655,0.8676 G +chr1 5831207 5831208 C/T 2 5,10 0.8978,0.8575 C +chr1 6200884 6200885 C 1 13 0.8346 A +chr1 6307254 6307255 C 1 11 0.8723 T +chr1 6621228 6621229 G/T 2 10,11 0.8405,0.8336 G +chr1 7094424 7094425 A 1 4 0.8578 G +chr1 7392593 7392594 C/T 2 15,25 0.8653,0.8644 C +chr1 7500089 7500090 G 1 13 0.8508 C +chr1 7911301 7911302 C/T 2 8,9 0.9113,0.8736 C +chr1 7954646 7954647 C/T 2 12,8 0.8365,0.8490 C +chr1 8027386 8027387 C/T 2 15,21 0.8669,0.8528 C +chr1 8549302 8549303 C/T 2 8,7 0.8606,0.8633 C +chr1 8932179 8932180 G/T 2 13,12 0.8136,0.8594 G +chr1 9016389 9016390 T 1 14 0.8590 C +chr1 9494443 9494444 T 1 6 0.8567 C +chr1 10615774 10615775 C 1 15 0.8684 T +chr1 10622975 10622976 T 1 4 0.8001 C +chr1 10782207 10782208 T 1 3 0.8402 C +chr1 12238146 12238147 A/G 2 4,9 0.8560,0.8449 G +chr1 12429037 12429038 A/G 2 8,6 0.8692,0.8863 A +chr1 12669902 12669903 C/T 2 10,24 0.8495,0.8653 T +chr1 13189040 13189041 A/T 2 8,4 0.8592,0.8868 A +chr1 14208570 14208571 A/G 2 10,8 0.8646,0.8495 G +chr1 14501554 14501555 A/G 2 17,26 0.8646,0.8663 G +chr1 15063865 15063866 A/G 2 9,18 0.8571,0.8272 G +chr1 15286095 15286096 G 1 21 0.8600 A +chr1 15441925 15441926 T 1 17 0.8402 C +chr1 15712178 15712179 A 1 14 0.8694 G +chr1 16207687 16207688 G 1 16 0.8512 C +chr1 16314956 16314957 A 1 31 0.8639 T +chr1 16476823 16476824 C/T 2 5,8 0.8822,0.8898 C +chr1 16730581 16730582 G 1 9 0.8232 C +chr1 17053721 17053722 T 1 66 0.8916 G +chr1 17053765 17053766 A/G 2 19,11 0.8246,0.8436 G +chr1 17408311 17408312 C 1 22 0.8786 G +chr1 17498098 17498099 C 1 3 0.7863 T +chr1 17715847 17715848 A 1 11 0.8438 G +chr1 18857430 18857431 C/T 2 17,14 0.8834,0.8586 C +chr1 19092742 19092743 G/T 2 16,10 0.8682,0.8678 G +chr1 19525584 19525585 C 1 12 0.8614 T +chr1 19921477 19921478 A/C 2 3,4 0.8781,0.8884 C +chr1 20044146 20044147 C/T 2 5,6 0.8571,0.8847 C +chr1 20269168 20269169 C/T 2 5,10 0.8936,0.8839 T +chr1 20947809 20947810 T 1 8 0.8416 C +chr1 21135182 21135183 A 1 13 0.8384 C +chr1 21941643 21941644 T 1 12 0.8389 G +chr1 22324976 22324977 C/T 2 9,6 0.8524,0.8158 C +chr1 22708791 22708792 A/T 2 8,12 0.8313,0.8557 T +chr1 22904350 22904351 A/G 2 10,4 0.8451,0.8523 A +chr1 22928348 22928349 G 1 7 0.8629 A +chr1 23039691 23039692 C 1 13 0.8484 G +chr1 24392068 24392069 T 1 4 0.8425 C +chr1 24851230 24851231 A/G 2 19,15 0.8794,0.8807 A +chr1 25158007 25158008 A/G 2 7,12 0.8350,0.8625 A +chr1 25250192 25250193 C/T 2 5,4 0.8613,0.8827 C +chr1 25349613 25349614 G 1 6 0.8963 A +chr1 25891773 25891774 C/T 2 9,7 0.8398,0.8869 C +chr1 25989060 25989061 A/G 2 14,5 0.8271,0.8143 G +chr1 25996483 25996484 A/G 2 25,17 0.7803,0.7880 A +chr1 26172110 26172111 A/G 2 24,13 0.8568,0.8740 A +chr1 26275739 26275740 C/T 2 10,16 0.8335,0.8656 T +chr1 26436230 26436231 A/C 2 18,14 0.8299,0.8245 C +chr1 27081694 27081695 A/G 2 7,10 0.8297,0.8288 G +chr1 27215078 27215079 C/T 2 9,5 0.8749,0.8190 T +chr1 27527485 27527486 A/G 2 3,5 0.8697,0.8867 A +chr1 28266702 28266703 C/T 2 4,5 0.8513,0.8812 C +chr1 28273015 28273016 G 1 23 0.7710 T +chr1 28548057 28548058 C 1 22 0.8518 G +chr1 28817596 28817597 G 1 17 0.8790 A +chr1 28833437 28833438 G/T 2 3,5 0.8753,0.8702 G +chr1 28848587 28848588 G/T 2 11,17 0.8629,0.8546 G +chr1 29140084 29140085 A/C 2 8,10 0.8493,0.8580 C +chr1 29788803 29788804 C 1 3 0.8525 T +chr1 30086425 30086426 A/G 2 15,14 0.8973,0.8948 A +chr1 30214408 30214409 A 1 36 0.8861 G +chr1 30311437 30311438 T 1 17 0.8655 C +chr1 30577637 30577638 A 1 12 0.8266 G +chr1 30764437 30764438 A 1 37 0.8368 C +chr1 30830488 30830489 C/T 2 11,7 0.8607,0.8011 C +chr1 30999686 30999687 A 1 23 0.8255 C +chr1 31004884 31004885 G 1 10 0.8221 A +chr1 31082488 31082489 C/G 2 11,13 0.8683,0.8446 G +chr1 31084258 31084259 C/T 2 9,10 0.8195,0.8752 T +chr1 31145761 31145762 C 1 40 0.8697 T +chr1 31858900 31858901 C 1 20 0.8667 T +chr1 31950701 31950702 A/G 2 10,12 0.8389,0.8720 G +chr1 32334351 32334352 C 1 8 0.8713 T +chr1 32689520 32689521 A/G 2 21,14 0.8642,0.8584 A +chr1 34054228 34054229 G 1 25 0.8579 A +chr1 34137111 34137112 T 1 19 0.8811 A +chr1 34255271 34255272 C/T 2 8,21 0.8586,0.8412 T +chr1 35503106 35503107 G/T 2 17,30 0.8577,0.8680 T +chr1 35568011 35568012 C 1 25 0.8800 T +chr1 35594503 35594504 A/C 2 6,3 0.8923,0.8708 C +chr1 37411518 37411519 A/G 2 10,6 0.8694,0.8395 G +chr1 37854804 37854805 A/G 2 9,9 0.8907,0.8479 A +chr1 38640339 38640340 C 1 33 0.8397 T +chr1 38714026 38714027 C/T 2 3,3 0.7870,0.8480 C +chr1 38942729 38942730 C/T 2 4,14 0.8413,0.8021 T +chr1 39473364 39473365 A/T 2 15,10 0.8351,0.8363 T +chr1 39582776 39582777 A/C 2 15,23 0.8690,0.8432 C +chr1 40168803 40168804 G/T 2 11,14 0.8791,0.8364 G +chr1 41916263 41916264 C/T 2 20,10 0.8697,0.8662 C +chr1 42448795 42448796 A/G 2 9,10 0.8430,0.8290 G +chr1 42685234 42685235 T 1 25 0.8526 C +chr1 42780260 42780261 G 1 31 0.8658 C +chr1 42877019 42877020 A/G 2 3,4 0.8024,0.7753 A +chr1 42908045 42908046 G 1 28 0.8490 A +chr1 43172101 43172102 A/C 2 7,5 0.8702,0.8660 A +chr1 44076468 44076469 A/G 2 5,8 0.9221,0.9035 G +chr1 44781151 44781152 C/T 2 13,11 0.8844,0.8831 C +chr1 44940836 44940837 A/T 2 12,7 0.8956,0.8714 T +chr1 45188972 45188973 G/T 2 12,4 0.8456,0.8680 G +chr1 45383375 45383376 G/T 2 11,13 0.8302,0.8630 G +chr1 45791153 45791154 A/G 2 7,8 0.8747,0.8606 G +chr1 47239882 47239883 A/G 2 5,3 0.9060,0.8570 G +chr1 47683527 47683528 T 1 27 0.8746 C +chr1 47841108 47841109 C 1 18 0.8608 T +chr1 47997657 47997658 C 1 14 0.9096 G +chr1 48521760 48521761 A/C 2 9,7 0.8805,0.8632 A +chr1 49140974 49140975 C/T 2 18,14 0.8159,0.8775 C +chr1 49364620 49364621 G 1 13 0.8580 A +chr1 49577482 49577483 C/T 2 7,3 0.8165,0.8696 C +chr1 49949033 49949034 C/T 2 8,9 0.8685,0.8852 T +chr1 51154057 51154058 C/T 2 15,17 0.8631,0.8589 T +chr1 51917770 51917771 G/T 2 11,12 0.8676,0.8527 G +chr1 52785701 52785702 G 1 7 0.7958 A +chr1 53310415 53310416 A/G 2 4,3 0.8619,0.8758 G +chr1 53517348 53517349 A/G 2 16,13 0.8435,0.8239 G +chr1 53587722 53587723 G 1 5 0.8247 C +chr1 54051897 54051898 C/T 2 7,13 0.8395,0.8902 T +chr1 54066375 54066376 A 1 3 0.8444 G +chr1 54161544 54161545 C/T 2 19,14 0.8679,0.8722 T +chr1 54661149 54661150 C/T 2 6,8 0.8480,0.8700 C +chr1 54961246 54961247 G 1 33 0.8740 A +chr1 55456929 55456930 G/T 2 6,14 0.8707,0.8839 T +chr1 55495994 55495995 C 1 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61632029 A 1 22 0.8376 G +chr1 62074485 62074486 A/G 2 18,18 0.8772,0.8548 A +chr1 62162170 62162171 G 1 4 0.9025 A +chr1 62471633 62471634 A/G 2 9,9 0.8844,0.8671 A +chr1 62691519 62691520 A/G 2 9,8 0.8581,0.8419 G +chr1 62768052 62768053 A/G 2 11,11 0.8326,0.8606 G +chr1 62868350 62868351 C/T 2 18,12 0.8546,0.8511 C +chr1 62963913 62963914 C 1 18 0.8595 G +chr1 63477653 63477654 C 1 29 0.8564 T +chr1 63963102 63963103 C/T 2 21,16 0.8460,0.8341 T +chr1 64188254 64188255 C/T 2 17,9 0.8485,0.8148 C +chr1 64284052 64284053 A/G 2 7,7 0.8400,0.8011 A +chr1 64420061 64420062 A/G 2 15,21 0.8546,0.8461 G +chr1 64717163 64717164 C/G 2 19,12 0.8583,0.8709 C +chr1 64765770 64765771 C/T 2 9,18 0.8373,0.8616 T +chr1 64800455 64800456 C/T 2 17,6 0.8759,0.8115 C +chr1 65042589 65042590 G/T 2 5,3 0.8591,0.8156 G +chr1 65103740 65103741 C/T 2 14,19 0.8434,0.8545 T +chr1 65711525 65711526 A/T 2 11,23 0.8326,0.8418 T +chr1 66705718 66705719 A/G 2 14,11 0.8762,0.8847 A +chr1 66946305 66946306 C 1 37 0.8304 G +chr1 67002116 67002117 C 1 15 0.8375 T +chr1 67094335 67094336 A 1 30 0.8477 G +chr1 67860626 67860627 A/G 2 16,12 0.8605,0.8525 A +chr1 68048718 68048719 A/G 2 13,14 0.8584,0.8531 A +chr1 68358176 68358177 C/T 2 12,18 0.8751,0.8600 C +chr1 69748509 69748510 A/G 2 21,12 0.8618,0.8674 A +chr1 69841275 69841276 G/T 2 9,6 0.8569,0.8747 G +chr1 70269052 70269053 A/T 2 16,18 0.8552,0.8495 T +chr1 71084849 71084850 A/G 2 10,6 0.8831,0.8905 A +chr1 71107799 71107800 A/G 2 10,16 0.9039,0.8827 A +chr1 72402879 72402880 A/G 2 13,12 0.8149,0.8678 G +chr1 72998810 72998811 C/T 2 6,6 0.8752,0.8567 C +chr1 73025215 73025216 A 1 19 0.8334 G +chr1 73742617 73742618 G/T 2 11,5 0.8673,0.8425 T +chr1 73799967 73799968 G/T 2 12,15 0.8343,0.8359 G +chr1 74010720 74010721 G/T 2 3,4 0.7179,0.7847 T +chr1 74572350 74572351 T 1 27 0.8473 C +chr1 74699911 74699912 A 1 8 0.8535 G +chr1 75638881 75638882 C/T 2 9,20 0.8840,0.8933 T +chr1 75969123 75969124 C/T 2 9,10 0.9070,0.8483 C +chr1 76356647 76356648 A 1 10 0.8293 G +chr1 76358465 76358466 G 1 19 0.8497 A +chr1 76441859 76441860 G 1 32 0.8756 A +chr1 76687274 76687275 A/G 2 18,13 0.8519,0.8690 A +chr1 77190283 77190284 G 1 13 0.8509 C +chr1 77361666 77361667 A 1 2 0.9443 T +chr1 77400544 77400545 A/G 2 13,15 0.8586,0.8392 G +chr1 77669303 77669304 C/T 2 5,3 0.8848,0.8601 T +chr1 78955604 78955605 A/G 2 13,12 0.8453,0.8620 G +chr1 79395056 79395057 A/C 2 12,12 0.8650,0.8670 C +chr1 79402253 79402254 A/G 2 6,12 0.8500,0.8537 G +chr1 79520060 79520061 T 1 3 0.8904 A +chr1 79762905 79762906 G 1 4 0.8775 T +chr1 80387731 80387732 T 1 21 0.8635 G +chr1 80727540 80727541 G/T 2 11,15 0.8510,0.8384 G +chr1 81863552 81863553 G/T 2 21,12 0.8742,0.8695 G +chr1 81898143 81898144 C/T 2 5,7 0.8314,0.8727 T +chr1 82047558 82047559 A/G 2 8,4 0.8136,0.8648 G +chr1 82554083 82554084 C 1 15 0.8327 T +chr1 82636239 82636240 A 1 3 0.9266 T +chr1 82709510 82709511 A/G 2 8,18 0.8825,0.8432 G +chr1 83028394 83028395 A/G 2 18,7 0.8747,0.8710 A 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96892654 96892655 C/T 2 11,9 0.8059,0.8190 C +chr1 96949371 96949372 A/C 2 10,15 0.8734,0.8663 C +chr1 97458721 97458722 C/T 2 18,17 0.8501,0.8396 C +chr1 97862236 97862237 C/T 2 9,10 0.9022,0.8590 T +chr1 97964121 97964122 G 1 27 0.8519 A +chr1 98762501 98762502 A/C 2 5,3 0.8493,0.8502 A +chr1 98764953 98764954 A/G 2 13,6 0.8371,0.8813 A +chr1 99495256 99495257 C 1 20 0.8363 A +chr1 99888286 99888287 A/G 2 6,10 0.7731,0.7865 A +chr1 100077931 100077932 A/T 2 5,10 0.8603,0.8637 T +chr1 101179630 101179631 A/C 2 8,17 0.8465,0.8305 C +chr1 101267805 101267806 G/T 2 3,8 0.6918,0.9129 T +chr1 101565234 101565235 C/T 2 11,15 0.8384,0.8466 C +chr1 101870921 101870922 G/T 2 13,10 0.8528,0.8307 T +chr1 102236121 102236122 A/C 2 21,15 0.8529,0.8536 C +chr1 102242396 102242397 C 1 18 0.8445 G +chr1 102458745 102458746 A 1 33 0.8921 T +chr1 102674166 102674167 C 1 18 0.8876 T +chr1 102870606 102870607 T 1 7 0.8874 C +chr1 103736308 103736309 C 1 11 0.8470 T +chr1 104945356 104945357 C/G 2 17,14 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242175271 G 1 11 0.8677 A +chr1 242226694 242226695 C 1 5 0.8324 G +chr1 242627620 242627621 A 1 36 0.8634 T +chr1 242941555 242941556 C/T 2 23,17 0.8456,0.8600 C +chr1 242964074 242964075 C/T 2 14,11 0.8481,0.8338 T +chr1 243004213 243004214 A/G 2 12,16 0.8438,0.8475 G +chr1 243623247 243623248 A/C 2 6,3 0.8820,0.7376 A +chr1 243835185 243835186 G 1 26 0.8901 A +chr1 244175327 244175328 A 1 22 0.8323 G +chr1 244238136 244238137 A/G 2 4,5 0.7997,0.8090 G +chr1 244259964 244259965 T 1 4 0.8251 C +chr1 244284218 244284219 G 1 16 0.8420 A +chr1 244444888 244444889 G 1 5 0.9162 C +chr1 244684266 244684267 C/G 2 21,16 0.8271,0.8245 G +chr1 244790675 244790676 C 1 8 0.8590 T +chr1 245319089 245319090 C/T 2 10,8 0.8435,0.8769 T +chr1 245447303 245447304 C 1 4 0.8860 A +chr1 245667834 245667835 C/T 2 8,5 0.8799,0.8389 T +chr1 245728972 245728973 C/T 2 6,5 0.8709,0.9142 T +chr1 246063974 246063975 C 1 32 0.8502 T +chr1 246299210 246299211 C/T 2 14,13 0.8731,0.8663 T +chr1 246329013 246329014 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2 7,13 0.8616,0.8676 T +chr2 9143011 9143012 A/T 2 5,10 0.8248,0.8300 A +chr2 9178379 9178380 T 1 29 0.8553 C +chr2 9773585 9773586 C/T 2 15,10 0.8741,0.8891 T +chr2 9805099 9805100 A/G 2 7,20 0.8302,0.8403 G +chr2 9967765 9967766 A/G 2 12,9 0.8679,0.8972 A +chr2 9970017 9970018 C/T 2 12,15 0.8615,0.8724 T +chr2 10356139 10356140 C/T 2 8,5 0.8023,0.8023 C +chr2 10613283 10613284 A 1 29 0.8376 G +chr2 11643829 11643830 A 1 15 0.7810 G +chr2 11834046 11834047 A 1 6 0.8677 G +chr2 11966615 11966616 A 1 4 0.8999 G +chr2 12146868 12146869 C/T 2 10,16 0.8749,0.8683 T +chr2 12227796 12227797 A/G 2 14,11 0.8742,0.8405 A +chr2 12364227 12364228 T 1 41 0.8428 C +chr2 13148264 13148265 C/T 2 4,14 0.8687,0.8741 T +chr2 13211442 13211443 C/T 2 19,8 0.8446,0.8316 T +chr2 13261985 13261986 T 1 13 0.8172 C +chr2 13520956 13520957 A/G 2 6,5 0.8646,0.8587 A +chr2 13653170 13653171 C/T 2 11,10 0.8684,0.8426 C +chr2 14331715 14331716 A/G 2 7,8 0.8851,0.8871 A +chr2 14904075 14904076 A 1 19 0.8775 G +chr2 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A +chr2 54913630 54913631 C/G 2 5,5 0.7846,0.7695 C +chr2 55075545 55075546 G 1 42 0.8782 A +chr2 55251373 55251374 A 1 51 0.8503 G +chr2 55307996 55307997 A 1 4 0.8707 G +chr2 55370488 55370489 C/G 2 13,12 0.8836,0.9030 G +chr2 56201625 56201626 A 1 34 0.8180 G +chr2 56724178 56724179 A/T 2 3,4 0.6182,0.7791 T +chr2 57600075 57600076 C/T 2 11,13 0.8644,0.8626 C +chr2 58296325 58296326 C 1 36 0.8607 A +chr2 58510033 58510034 T 1 22 0.8861 C +chr2 58589194 58589195 T 1 29 0.8725 C +chr2 58779120 58779121 T 1 2 0.8633 C +chr2 58792231 58792232 T 1 13 0.8380 C +chr2 59066562 59066563 G 1 24 0.8339 A +chr2 59293312 59293313 C/G 2 18,11 0.8240,0.8519 G +chr2 60071276 60071277 C/T 2 10,14 0.8460,0.8585 T +chr2 60519256 60519257 C/T 2 13,13 0.8735,0.8543 C +chr2 60547566 60547567 G 1 22 0.8584 A +chr2 60817253 60817254 C/T 2 12,11 0.8823,0.8863 C +chr2 61311118 61311119 A/G 2 6,9 0.8739,0.8454 G +chr2 61374148 61374149 C 1 8 0.8641 T +chr2 61932435 61932436 A 1 17 0.8533 G +chr2 62023583 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 66212287 66212288 G 1 3 0.8031 C 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242323119 C/T 2 9,20 0.8814,0.8456 T +chr2 242625733 242625734 G 1 21 0.8778 C +chr2 242787513 242787514 C/T 2 11,9 0.8774,0.8763 C +chr3 614688 614689 C/T 2 14,8 0.8778,0.8334 C +chr3 750388 750389 C/T 2 3,4 0.8882,0.8724 C +chr3 888994 888995 T 1 14 0.8456 G +chr3 1328767 1328768 G 1 8 0.9129 T +chr3 1348569 1348570 A/T 2 8,9 0.8716,0.8623 A +chr3 1587859 1587860 C/T 2 13,10 0.8723,0.8819 T +chr3 1756870 1756871 C/G 2 21,10 0.8555,0.8576 G +chr3 1862779 1862780 C/T 2 7,6 0.8652,0.8616 C +chr3 1970016 1970017 C/T 2 13,24 0.8324,0.8259 T +chr3 1994643 1994644 A 1 11 0.8751 C +chr3 2032901 2032902 C/T 2 5,5 0.8223,0.8057 C +chr3 2139921 2139922 C 1 8 0.8561 A +chr3 2275005 2275006 C/T 2 18,14 0.8521,0.8677 C +chr3 2317280 2317281 A 1 9 0.8385 G +chr3 2470718 2470719 G 1 14 0.9008 A +chr3 2744662 2744663 C/G 2 11,11 0.8255,0.8100 G +chr3 2875926 2875927 C/G 2 12,7 0.8411,0.8453 C +chr3 2890537 2890538 A/G 2 10,16 0.8511,0.8660 G +chr3 2907096 2907097 A 1 14 0.8760 G +chr3 2953325 2953326 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51201411 51201412 C 1 28 0.8655 T +chr3 52720079 52720080 C 1 15 0.8341 A +chr3 52971578 52971579 A/G 2 8,18 0.8434,0.8282 G +chr3 53084288 53084289 G 1 9 0.8820 T +chr3 54228290 54228291 A/T 2 15,13 0.8335,0.7837 A +chr3 54267623 54267624 C/T 2 14,22 0.8790,0.8801 T +chr3 54499049 54499050 T 1 9 0.9304 C +chr3 54926622 54926623 A 1 10 0.8497 C +chr3 54929650 54929651 A/C 2 16,20 0.8356,0.8377 C +chr3 55119275 55119276 A/G 2 21,14 0.8659,0.8879 G +chr3 55181875 55181876 C/T 2 2,4 0.9610,0.8514 T +chr3 55492049 55492050 T 1 26 0.8568 C +chr3 55936700 55936701 A/G 2 15,24 0.8447,0.8462 A +chr3 56135450 56135451 A/G 2 9,18 0.8532,0.8599 A +chr3 56161289 56161290 A 1 30 0.8452 T +chr3 56228601 56228602 A/G 2 8,6 0.7838,0.8678 G +chr3 56263255 56263256 C 1 22 0.8632 T +chr3 56502077 56502078 T 1 12 0.8276 G +chr3 56650707 56650708 A 1 16 0.9014 G +chr3 57278672 57278673 G 1 26 0.8841 A +chr3 57394484 57394485 C 1 4 0.8452 T +chr3 57455696 57455697 C/T 2 10,6 0.8550,0.7793 C +chr3 57701936 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2 11,3 0.8728,0.8114 T +chr4 154162668 154162669 C/T 2 11,20 0.8884,0.8761 T +chr4 154492165 154492166 A/G 2 10,8 0.8857,0.8432 A +chr4 154706015 154706016 A/G 2 16,15 0.8330,0.8504 G +chr4 154714115 154714116 A/T 2 4,6 0.8315,0.8646 A +chr4 154829155 154829156 A/G 2 23,20 0.8610,0.8954 G +chr4 155162788 155162789 A/G 2 5,7 0.8406,0.8365 A +chr4 155430934 155430935 A 1 4 0.8594 T +chr4 156281668 156281669 C/T 2 4,4 0.8742,0.7787 C +chr4 157108351 157108352 A/C 2 6,9 0.8964,0.8525 A +chr4 157233214 157233215 C/T 2 12,19 0.8571,0.8818 T +chr4 157563568 157563569 C/T 2 17,15 0.8041,0.8083 C +chr4 157633621 157633622 T 1 13 0.8661 C +chr4 157746164 157746165 C/T 2 11,7 0.8252,0.8430 C +chr4 157811440 157811441 A/G 2 9,9 0.8133,0.8443 G +chr4 157984813 157984814 T 1 23 0.8748 C +chr4 158394831 158394832 C 1 31 0.8581 T +chr4 158932875 158932876 G 1 24 0.8827 T +chr4 159032439 159032440 A 1 23 0.8567 G +chr4 159541402 159541403 G 1 28 0.8530 A +chr4 159545147 159545148 A 1 3 0.8041 G +chr4 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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 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2 9,7 0.8012,0.8147 C +chr8 3964313 3964314 C 1 7 0.8880 T +chr8 4031325 4031326 G 1 36 0.8619 C +chr8 4056479 4056480 T 1 3 0.8680 A +chr8 4349662 4349663 G 1 23 0.8687 C +chr8 4508702 4508703 A/G 2 12,11 0.8784,0.8711 A +chr8 4587366 4587367 C/T 2 5,7 0.8846,0.8801 T +chr8 4655592 4655593 C/G 2 6,3 0.8913,0.8942 C +chr8 4782051 4782052 G 1 2 0.8920 C +chr8 4844403 4844404 A/G 2 11,16 0.8211,0.8581 G +chr8 4951063 4951064 A 1 24 0.8352 G +chr8 5070850 5070851 A/G 2 12,13 0.8614,0.8400 G +chr8 5089024 5089025 G 1 6 0.7985 T +chr8 5105060 5105061 G 1 35 0.8594 T +chr8 5157362 5157363 C/T 2 15,13 0.8782,0.8760 T +chr8 5347119 5347120 A/G 2 9,8 0.8035,0.7895 A +chr8 5586185 5586186 C/T 2 5,6 0.8277,0.8825 C +chr8 5671310 5671311 C/T 2 22,8 0.8333,0.8486 C +chr8 5899513 5899514 T 1 28 0.8764 G +chr8 5976167 5976168 A/C 2 4,4 0.8620,0.8850 C +chr8 6024174 6024175 G 1 37 0.8582 A +chr8 6069171 6069172 T 1 5 0.8682 A +chr8 6165823 6165824 A/G 2 11,12 0.8334,0.8654 G +chr8 6251985 6251986 G/T 2 6,3 0.7772,0.8402 T +chr8 6463002 6463003 G 1 16 0.8656 A +chr8 6497752 6497753 C/G 2 16,8 0.8444,0.8525 C +chr8 6505704 6505705 A/T 2 10,3 0.8849,0.8805 A +chr8 6561255 6561256 A/G 2 4,3 0.8675,0.8333 G +chr8 6658469 6658470 C 1 4 0.8445 G +chr8 6684000 6684001 A/G 2 15,18 0.8797,0.8956 A +chr8 6722350 6722351 A 1 13 0.8478 T +chr8 6754918 6754919 G 1 24 0.8705 C +chr8 6781685 6781686 C 1 5 0.8968 T +chr8 6879884 6879885 C/T 2 20,7 0.8479,0.8676 C +chr8 7831188 7831189 G 1 2 0.8670 C +chr8 8192830 8192831 C/T 2 12,18 0.8517,0.8895 T +chr8 8271709 8271710 C/T 2 12,24 0.8669,0.8689 T +chr8 8319341 8319342 A/C 2 12,21 0.8463,0.8208 C +chr8 8543543 8543544 A/G 2 4,4 0.9012,0.8815 A +chr8 8610782 8610783 C 1 5 0.8035 A +chr8 8861183 8861184 A/C 2 20,16 0.8267,0.8540 C +chr8 8932550 8932551 C/G 2 17,24 0.8846,0.8732 C +chr8 9085514 9085515 A/C 2 5,6 0.9011,0.8698 C +chr8 9155684 9155685 C/T 2 7,3 0.8583,0.8748 C +chr8 9225846 9225847 A/G 2 8,9 0.8624,0.7734 A +chr8 9687552 9687553 C/G 2 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0.8664,0.8669 C +chr8 24580755 24580756 A/G 2 12,16 0.8642,0.8700 G +chr8 24716593 24716594 G 1 31 0.8490 A +chr8 24741724 24741725 A 1 30 0.8745 G +chr8 25054133 25054134 A/G 2 8,7 0.8235,0.8083 A +chr8 25227225 25227226 G/T 2 8,15 0.9057,0.8852 G +chr8 25645065 25645066 C/T 2 18,10 0.8428,0.8092 C +chr8 25654047 25654048 A/T 2 8,11 0.8762,0.8630 A +chr8 25760359 25760360 G/T 2 18,18 0.8845,0.8722 G +chr8 25900308 25900309 G/T 2 15,15 0.8661,0.8705 G +chr8 26355746 26355747 C/T 2 16,10 0.8496,0.8366 C +chr8 26369268 26369269 A/G 2 10,4 0.8525,0.8291 G +chr8 26543313 26543314 A 1 26 0.8548 G +chr8 26819162 26819163 C 1 33 0.8730 T +chr8 26881354 26881355 G/T 2 28,20 0.8715,0.8552 G +chr8 27077741 27077742 A/G 2 18,10 0.8961,0.8848 A +chr8 27234932 27234933 A/G 2 10,11 0.8716,0.8747 G +chr8 27563688 27563689 A/G 2 3,8 0.8026,0.8981 G +chr8 27600973 27600974 C/T 2 13,15 0.9085,0.8934 T +chr8 27633554 27633555 G 1 19 0.8634 A +chr8 27722399 27722400 A/G 2 6,6 0.8692,0.8361 A +chr8 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C 1 20 0.8322 T +chr11 5349061 5349062 C/T 2 13,8 0.8541,0.8181 T +chr11 5987695 5987696 T 1 24 0.7884 C +chr11 6005758 6005759 A/G 2 17,11 0.8212,0.8210 G +chr11 6428016 6428017 A/C 2 8,9 0.8561,0.8779 C +chr11 6920772 6920773 C/G 2 10,10 0.8638,0.8563 G +chr11 7794975 7794976 A 1 16 0.8435 T +chr11 7850955 7850956 G 1 17 0.8430 C +chr11 7901367 7901368 T 1 20 0.8227 C +chr11 7916070 7916071 C/T 2 7,5 0.9275,0.8635 C +chr11 7927053 7927054 A/T 2 15,14 0.8726,0.8701 A +chr11 7970049 7970050 C/T 2 13,11 0.8427,0.9007 C +chr11 8104485 8104486 C/T 2 16,15 0.8869,0.8790 T +chr11 8269312 8269313 C/T 2 11,6 0.8576,0.8657 T +chr11 8529276 8529277 A 1 36 0.8565 G +chr11 8529837 8529838 T 1 8 0.8454 C +chr11 8549622 8549623 T 1 28 0.8390 C +chr11 9024851 9024852 A 1 19 0.8947 G +chr11 9674914 9674915 C/T 2 7,5 0.8088,0.8938 T +chr11 9697343 9697344 C/T 2 6,10 0.8843,0.8548 T +chr11 9882345 9882346 G 1 18 0.8532 A +chr11 10408115 10408116 G 1 13 0.7903 C +chr11 10769020 10769021 C/T 2 6,6 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65335512 T 1 6 0.8041 C +chr18 65471580 65471581 A/G 2 5,13 0.8305,0.8417 A +chr18 65615782 65615783 A/G 2 15,13 0.8661,0.8751 G +chr18 65703472 65703473 G 1 21 0.8406 A +chr18 66313773 66313774 C 1 18 0.8845 G +chr18 67186056 67186057 A 1 29 0.8573 G +chr18 67259873 67259874 A/T 2 9,5 0.8016,0.8197 T +chr18 67287028 67287029 G 1 21 0.8284 C +chr18 67354468 67354469 A 1 12 0.8768 G +chr18 67478876 67478877 A 1 3 0.8511 T +chr18 67489883 67489884 C/G 2 10,16 0.8126,0.8466 G +chr18 67507984 67507985 C 1 27 0.8426 T +chr18 67547413 67547414 G 1 16 0.8840 T +chr18 67852535 67852536 C/G 2 16,22 0.8744,0.8735 G +chr18 68033941 68033942 C/T 2 6,20 0.8258,0.8901 T +chr18 68501662 68501663 A/T 2 17,10 0.8421,0.8436 T +chr18 68718615 68718616 C/T 2 4,10 0.8403,0.8951 T +chr18 68757854 68757855 C 1 4 0.8020 T +chr18 68878233 68878234 G 1 18 0.8660 A +chr18 68906841 68906842 G/T 2 16,14 0.8335,0.8211 G +chr18 69021430 69021431 G/T 2 23,14 0.8670,0.8658 G +chr18 69038775 69038776 T 1 9 0.8336 G 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