/usr/lib/R/site-library/VariantAnnotation/extdata/gl_chr1.vcf is in r-bioc-variantannotation 1.20.2-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | ##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">
##reference=GRCh37
##source_20120923.1=/nfs/public/rw/ensembl/vcftools/bin/vcf-subset -c NA06984,NA06986,NA06989,NA06994,NA07000,NA07037,NA07048,NA07051,NA07056,NA07347,NA07357,NA10847,NA10851,NA11829,NA11830,NA11831,NA11843,NA11892,NA11893,NA11894,NA11919,NA11920,NA11930,NA11931,NA11932,NA11933,NA11992,NA11993,NA11994,NA11995,NA12003,NA12004,NA12006,NA12043,NA12044,NA12045,NA12046,NA12058,NA12144,NA12154,NA12155,NA12249,NA12272,NA12273,NA12275,NA12282,NA12283,NA12286,NA12287,NA12340,NA12341,NA12342,NA12347,NA12348,NA12383,NA12399,NA12400,NA12413,NA12489,NA12546,NA12716,NA12717,NA12718,NA12748,NA12749,NA12750,NA12751,NA12761,NA12763,NA12775,NA12777,NA12778,NA12812,NA12814,NA12815,NA12827,NA12829,NA12830,NA12842,NA12843,NA12872,NA12873,NA12874,NA12889,NA12890 /net/isilonP/public/rw/ensembl/1000genomes/release-12/tmp/slicer/1.1-50000.ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA06984 NA06986 NA06989 NA06994 NA07000 NA07037 NA07048 NA07051 NA07056 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11843 NA11892 NA11893 NA11894 NA11919 NA11920 NA11930 NA11931 NA11932 NA11933 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12006 NA12043 NA12044 NA12045 NA12046 NA12058 NA12144 NA12154 NA12155 NA12249 NA12272 NA12273 NA12275 NA12282 NA12283 NA12286 NA12287 NA12340 NA12341 NA12342 NA12347 NA12348 NA12383 NA12399 NA12400 NA12413 NA12489 NA12546 NA12716 NA12717 NA12718 NA12748 NA12749 NA12750 NA12751 NA12761 NA12763 NA12775 NA12777 NA12778 NA12812 NA12814 NA12815 NA12827 NA12829 NA12830 NA12842 NA12843 NA12872 NA12873 NA12874 NA12889 NA12890
1 10583 rs58108140 G A 100 PASS AA=.;AC=37;AF=0.14;AFR_AF=0.04;AMR_AF=0.17;AN=170;ASN_AF=0.13;AVGPOST=0.7707;ERATE=0.0161;EUR_AF=0.21;LDAF=0.2327;RSQ=0.4319;SNPSOURCE=LOWCOV;THETA=0.0046;VT=SNP GT:DS:GL 0|1:1.250:-4.70,-0.58,-0.13 0|1:0.750:-1.15,-0.10,-0.84 0|1:1.000:-2.05,-0.00,-3.27 0|0:0.450:-0.48,-0.48,-0.48 0|0:0.400:-0.28,-0.44,-0.96 0|0:0.550:-0.48,-0.48,-0.48 0|1:1.000:-1.93,-0.02,-1.45 0|0:0.100:-0.02,-1.44,-5.00 0|1:1.150:-2.72,-0.46,-0.19 0|0:0.400:-0.48,-0.48,-0.48 0|0:0.000:-0.05,-0.96,-5.00 0|1:0.550:-0.48,-0.18,-2.28 0|0:0.050:-0.01,-1.50,-5.00 0|0:0.200:-0.05,-0.94,-4.70 0|1:1.000:-0.90,-0.06,-5.00 0|0:0.350:-0.48,-0.17,-4.40 0|0:0.400:-0.48,-0.48,-0.48 0|0:0.150:-0.11,-0.64,-4.10 0|0:0.100:-0.04,-1.08,-5.00 0|0:0.250:-0.48,-0.48,-0.48 0|1:1.050:-0.93,-0.39,-0.32 0|0:0.150:-0.48,-0.48,-0.48 0|1:0.850:-0.76,-0.08,-5.00 0|1:0.550:-0.48,-0.48,-0.48 0|0:0.100:-0.11,-0.64,-3.40 0|1:0.850:-0.62,-0.12,-5.00 0|0:0.550:-0.48,-0.48,-0.48 0|0:0.150:-0.13,-0.58,-2.73 0|0:0.000:-0.07,-0.85,-5.00 0|1:0.850:-1.34,-0.08,-0.92 0|0:0.500:-0.29,-0.43,-0.95 0|0:0.550:-0.48,-0.48,-0.48 0|1:1.000:-3.15,-0.01,-1.70 0|0:0.350:-0.48,-0.48,-0.48 0|1:0.900:-1.16,-0.10,-0.89 0|0:0.350:-0.18,-0.48,-1.76 0|0:0.550:-0.477139,-0.477113,-0.477113 0|1:1.000:-4.70,-0.00,-5.00 0|0:0.100:-0.04,-1.04,-5.00 0|1:1.000:-2.80,-0.00,-2.27 0|0:0.150:-0.08,-0.78,-5.00 0|0:0.450:-0.48,-0.48,-0.48 0|1:0.750:-0.48,-0.48,-0.48 0|0:0.400:-0.18,-0.48,-2.05 0|0:0.200:-0.19,-0.47,-2.13 0|0:0.050:-0.0744919,-0.802609,-4.09691 0|1:0.800:-1.34,-0.02,-3.52 0|1:0.550:-0.46,-0.19,-5.00 0|1:0.800:-0.48,-0.48,-0.48 0|0:0.700:-0.48,-0.48,-0.48 0|0:0.250:-0.11,-0.65,-3.92 0|1:1.000:-5.00,-0.00,-3.05 0|1:1.000:-3.09,-0.00,-5.00 0|1:1.000:-5.00,0.00,-5.00 0|0:0.250:-0.12,-0.63,-3.74 0|0:0.350:-0.19,-0.46,-2.34 0|1:0.750:-0.477139,-0.477113,-0.477113 0|1:0.800:-1.38,-0.02,-4.70 0|0:0.200:-0.11,-0.65,-3.36 0|1:1.000:-5.00,-0.00,-3.80 0|1:0.650:-0.48,-0.48,-0.48 0|0:0.550:-0.48,-0.48,-0.48 0|1:1.000:-5.00,-0.00,-2.37 0|0:0.150:-0.06,-0.92,-5.00 0|0:0.000:-0.01,-1.54,-5.00 0|1:1.100:-1.78,-0.40,-0.23 0|0:0.500:-0.48,-0.48,-0.48 0|0:0.500:-0.48,-0.48,-0.48 0|0:0.700:-0.48,-0.48,-0.48 0|1:1.150:-4.70,-0.07,-0.85 0|0:0.100:-0.06,-0.87,-5.00 0|1:1.100:-4.70,-0.14,-0.55 0|0:0.350:-0.14,-0.56,-2.82 0|0:0.050:-0.05,-0.97,-5.00 0|0:0.000:-0.11,-0.65,-3.40 0|1:0.800:-0.70,-0.10,-5.00 0|1:1.000:-3.22181,-0.00425079,-2.03905 0|1:1.000:-5.00,0.00,-5.00 0|0:0.150:-0.14,-0.55,-3.52 0|1:1.000:-1.62,-0.01,-2.66 0|1:1.200:-2.36,-0.21,-0.42 0|0:0.100:-0.08,-0.77,-4.70 0|0:0.100:-0.02,-1.27,-5.00 0|1:1.000:-4.10,-0.00,-4.40 0|0:0.150:-0.05,-0.99,-5.00
1 10611 rs189107123 C . 100 PASS AA=.;AC=0;AF=0.02;AFR_AF=0.01;AMR_AF=0.03;AN=170;ASN_AF=0.01;AVGPOST=0.9330;ERATE=0.0048;EUR_AF=0.02;LDAF=0.0479;RSQ=0.3475;SNPSOURCE=LOWCOV;THETA=0.0077;VT=SNP GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.24,-0.41,-1.44 0|0:0.050:-0.19,-0.45,-2.25 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.12,-0.63,-3.10 0|0:0.000:-0.19,-0.45,-2.23 0|0:0.000:-0.19,-0.45,-2.04 0|0:0.000:-0.12,-0.62,-4.40 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.41,-0.45,-0.59 0|0:0.000:-0.19,-0.46,-2.27 0|0:0.000:-0.04,-1.06,-5.00 0|0:0.000:-0.19,-0.48,-1.56 0|0:0.000:-0.11,-0.65,-4.10 0|0:0.000:-0.20,-0.45,-1.96 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.07,-0.85,-5.00 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.000:-0.24,-0.41,-1.44 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.11,-0.66,-4.40 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.050:-0.40,-0.42,-0.66 0|0:0.000:-0.01,-1.59,-5.00 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.19,-0.47,-1.81 0|0:0.000:-0.04,-1.08,-5.00 0|0:0.000:-0.19,-0.47,-1.69 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.19,-0.46,-1.80 0|0:0.000:-0.16,-0.52,-2.28 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.050:-0.22,-0.44,-1.41 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.000:-0.165516,-0.505484,-2.33348 0|0:0.000:-0.07,-0.81,-5.00 0|0:0.050:-0.13,-0.58,-2.79 0|0:0.000:-0.13,-0.60,-2.98 0|0:0.050:-0.14,-0.56,-3.05 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.050:-0.18,-0.48,-2.04 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.0666747,-0.846856,-4.39794 0|0:0.000:-0.12,-0.63,-3.59 0|0:0.000:-0.01,-1.48,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.20,-0.45,-2.01 0|0:0.000:-0.19,-0.46,-2.39 0|0:0.000:-0.11,-0.66,-4.00 0|0:0.000:-0.01,-1.70,-5.00 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.477139,-0.477113,-0.477113 0|0:0.000:-0.03,-1.12,-5.00 0|0:0.050:-0.18,-0.48,-1.99 0|0:0.050:-0.07,-0.85,-5.00 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.01,-1.71,-5.00 0|0:0.000:-0.09,-0.73,-4.22 0|0:0.050:-0.20,-0.47,-1.57 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.000:-0.12,-0.63,-3.66 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.07,-0.82,-5.00 0|0:0.000:-0.18,-0.48,-2.27 0|0:0.000:-0.14,-0.56,-2.82 0|0:0.000:-0.13,-0.58,-2.97 0|0:0.000:-0.03,-1.13,-5.00 0|0:0.000:-0.0503466,-0.960745,-5 0|0:0.000:-0.00,-4.40,-5.00 0|0:0.050:-0.20,-0.45,-2.25 0|0:0.150:-0.20,-0.45,-1.94 0|0:0.050:-0.13,-0.58,-2.84 0|0:0.150:-0.18,-0.48,-2.21 0|0:0.000:-0.05,-0.97,-5.00 0|0:0.050:-0.19,-0.46,-2.12 0|0:0.000:-0.05,-1.00,-5.00
1 13302 rs180734498 C T 100 PASS AA=.;AC=20;AF=0.11;AFR_AF=0.21;AMR_AF=0.08;AN=170;ASN_AF=0.02;AVGPOST=0.8895;ERATE=0.0058;EUR_AF=0.14;LDAF=0.1573;RSQ=0.6281;SNPSOURCE=LOWCOV;THETA=0.0048;VT=SNP GT:DS:GL 0|1:1.000:-2.01,-0.40,-0.23 0|0:0.000:-0.04,-1.08,-5.00 0|0:0.000:-0.08,-0.77,-5.00 0|0:0.100:-0.20,-0.45,-1.73 0|1:0.950:-1.68,-0.40,-0.24 0|1:0.850:-0.42,-0.21,-5.00 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.100:-0.13,-0.60,-4.10 1|0:0.850:-1.15,-0.03,-5.00 0|0:0.100:-0.26,-0.41,-1.17 0|0:0.100:-0.08,-0.79,-4.70 0|0:0.200:-0.20,-0.45,-2.12 0|1:0.950:-2.54,-0.00,-5.00 0|1:1.000:-5.00,0.00,-5.00 0|0:0.000:-0.00,-2.09,-5.00 0|1:0.750:-0.63,-0.12,-5.00 0|0:0.000:-0.07,-0.84,-5.00 0|0:0.350:-0.26,-0.34,-5.00 0|1:1.000:-4.22,-0.00,-5.00 0|0:0.150:-0.31,-0.41,-0.92 0|0:0.200:-0.20,-0.45,-2.02 0|0:0.150:-0.12,-0.61,-3.27 0|0:0.000:-0.01,-1.49,-5.00 0|0:0.400:-0.48,-0.48,-0.48 0|0:0.250:-0.48,-0.48,-0.48 0|1:1.000:-1.93,-0.03,-1.29 0|0:0.050:-0.11,-0.65,-3.80 0|0:0.300:-0.16,-0.52,-5.00 0|0:0.000:-0.05,-1.01,-5.00 0|0:0.500:-0.48,-0.48,-0.48 0|0:0.450:-0.22,-0.40,-3.92 0|0:0.050:-0.04,-1.03,-4.40 1|0:1.000:-3.55,-0.00,-5.00 0|0:0.250:-0.21,-0.46,-1.39 0|0:0.250:-0.22,-0.46,-1.31 0|0:0.200:-0.19,-0.45,-2.11 0|0:0.050:-0.130463,-0.587405,-3.04576 0|0:0.150:-0.20,-0.44,-2.36 0|0:0.300:-0.20,-0.46,-1.76 0|0:0.100:-0.03,-1.18,-5.00 1|0:1.000:-4.40,-0.00,-2.95 0|0:0.300:-0.48,-0.48,-0.48 0|0:0.300:-0.48,-0.48,-0.48 0|0:0.400:-0.48,-0.48,-0.48 0|1:1.250:-4.70,-0.62,-0.12 0|0:0.000:-0.0146544,-1.47912,-5 0|0:0.100:-0.11,-0.66,-3.85 0|0:0.100:-0.05,-0.95,-5.00 0|0:0.200:-0.38,-0.43,-0.67 0|0:0.300:-0.48,-0.48,-0.48 0|0:0.350:-0.20,-0.45,-2.02 1|0:1.000:-4.00,-0.02,-1.37 1|0:0.650:-0.86,-0.06,-5.00 0|0:0.000:-0.00,-2.05,-5.00 0|0:0.000:-0.02,-1.46,-5.00 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.000:-0.00528701,-1.91721,-5 0|0:0.100:-0.09,-0.74,-5.00 0|1:0.700:-0.80,-0.07,-4.70 0|1:0.850:-1.28,-0.02,-2.69 0|0:0.300:-0.48,-0.48,-0.48 0|0:0.300:-0.48,-0.48,-0.48 0|0:0.050:-0.03,-1.24,-5.00 0|0:0.300:-0.21,-0.44,-1.66 0|0:0.150:-0.21,-0.46,-1.51 1|0:0.900:-1.40,-0.38,-0.26 0|0:0.700:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.100:-0.15,-0.54,-2.92 0|0:0.150:-0.23,-0.42,-1.56 0|0:0.000:-0.01,-1.61,-5.00 1|0:0.750:-1.07,-0.04,-4.10 0|0:0.350:-0.67,-0.10,-5.00 0|1:1.000:-2.36,-0.00,-4.70 0|1:1.000:-3.52,-0.00,-3.10 0|0:0.100:-0.08,-0.78,-5.00 0|0:0.000:-0.00338326,-2.11014,-5 0|0:0.100:-0.18,-0.48,-2.37 0|0:0.000:-0.04,-1.01,-5.00 0|0:0.100:-0.05,-0.94,-5.00 0|0:0.050:-0.06,-0.90,-3.74 0|0:0.250:-0.32,-0.28,-5.00 0|0:0.250:-0.10,-0.70,-2.78 0|0:0.550:-0.48,-0.48,-0.48 0|0:0.050:-0.13,-0.59,-2.97
1 13327 rs144762171 G . 100 PASS AA=.;AC=0;AF=0.03;AFR_AF=0.02;AMR_AF=0.03;AN=170;ASN_AF=0.02;AVGPOST=0.9698;ERATE=0.0012;EUR_AF=0.04;LDAF=0.0359;RSQ=0.6482;SNPSOURCE=LOWCOV;THETA=0.0204;VT=SNP GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.00,-3.07,-5.00 0|0:0.000:-0.10,-0.68,-4.70 0|0:0.050:-0.21,-0.45,-1.67 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.00,-3.36,-5.00 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.07,-0.82,-5.00 0|0:0.000:-0.00,-4.70,-5.00 0|0:0.000:-0.26,-0.41,-1.19 0|0:0.000:-0.02,-1.29,-5.00 0|0:0.000:-0.03,-1.24,-5.00 0|0:0.000:-0.00,-2.01,-5.00 0|0:0.000:0.00,-5.00,-5.00 0|0:0.000:-0.00,-4.70,-5.00 0|0:0.000:-0.01,-1.90,-5.00 0|0:0.000:-0.02,-1.36,-5.00 0|0:0.000:-0.00,-2.97,-5.00 0|0:0.000:-0.00,-2.54,-5.00 0|0:0.050:-0.30,-0.41,-0.92 0|0:0.000:-0.20,-0.45,-1.99 0|0:0.000:-0.12,-0.63,-3.44 0|0:0.000:-0.00,-2.02,-5.00 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.32,-0.41,-0.88 0|0:0.250:-0.52,-0.16,-5.00 0|0:0.000:-0.12,-0.62,-4.70 0|0:0.000:-0.00,-3.25,-5.00 0|0:0.000:-0.02,-1.27,-5.00 0|0:0.050:-0.40,-0.45,-0.60 0|0:0.000:-0.00,-2.15,-5.00 0|0:0.000:-0.01,-1.55,-5.00 0|0:0.100:-0.18,-0.48,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.30,-0.41,-0.97 0|0:0.000:-0.0397766,-1.05789,-5 0|0:0.000:-0.19,-0.45,-2.53 0|0:0.000:-0.00,-2.48,-5.00 0|0:0.000:-0.00,-4.40,-5.00 0|0:0.000:-0.01,-1.56,-5.00 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.000:-0.00919955,-1.67861,-5 0|0:0.000:-0.01,-1.73,-5.00 0|0:0.000:-0.00,-2.82,-5.00 0|0:0.000:-0.38,-0.43,-0.68 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.050:-0.19,-0.45,-2.03 0|0:0.000:-0.07,-0.82,-5.00 0|0:0.000:-0.00,-2.34,-5.00 0|0:0.000:-0.00,-3.52,-5.00 0|0:0.000:-0.00,-2.08,-5.00 0|0:0.000:-0.12,-0.61,-3.92 0|0:0.000:-0.00418936,-2.01773,-5 0|0:0.000:-0.00,-4.40,-5.00 0|0:0.000:-0.00,-2.11,-5.00 0|0:0.000:-0.06,-0.86,-5.00 0|0:0.000:-0.00,-2.01,-5.00 0|0:0.050:-0.12,-0.63,-3.74 0|0:0.000:-0.00,-2.29,-5.00 0|0:0.000:-0.13,-0.60,-3.19 0|0:0.000:-0.20,-0.47,-1.57 0|0:0.050:-0.07,-0.84,-5.00 0|0:0.150:-0.22,-0.43,-1.69 0|0:0.000:-0.08,-0.80,-5.00 0|0:0.000:-0.04,-1.02,-5.00 0|0:0.050:-0.20,-0.45,-1.99 0|0:0.000:-0.00,-2.98,-5.00 0|0:0.000:-0.01,-1.57,-5.00 0|0:0.000:-0.02,-1.31,-5.00 0|0:0.000:-0.00,-2.63,-5.00 0|0:0.100:-0.11,-0.65,-5.00 0|0:0.000:-0.00,-3.08,-5.00 0|0:0.000:0,-5,-5 0|0:0.000:-0.02,-1.26,-5.00 0|0:0.000:-0.00,-2.69,-5.00 0|0:0.000:-0.02,-1.46,-5.00 0|0:0.050:-0.02,-1.29,-5.00 0|0:0.000:-0.00,-2.25,-5.00 0|0:0.000:-0.03,-1.20,-5.00 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.02,-1.28,-5.00
1 13957 rs201747181 TC . 28 PASS AA=TC;AC=0;AF=0.02;AFR_AF=0.02;AMR_AF=0.02;AN=170;ASN_AF=0.01;AVGPOST=0.8711;ERATE=0.0065;EUR_AF=0.02;LDAF=0.0788;RSQ=0.2501;THETA=0.0100;VT=INDEL GT:DS:GL 0|0:0.200:0,0,0 0|0:0.150:0,0,0 0|0:0.100:0,0,0 0|0:0.200:0,0,0 0|0:0.150:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.200:0,0,0 0|0:0.250:0,0,0 0|0:0.050:0,0,0 0|0:0.250:0,0,0 0|0:0.250:0,0,0 0|0:0.250:0,0,0 0|0:0.300:0,0,0 0|0:0.250:0.00,-0.30,-4.10 0|0:0.300:0,0,0 0|0:0.250:0,0,0 0|0:0.050:0.00,-0.60,-8.20 0|0:0.250:0,0,0 0|0:0.100:0,0,0 0|0:0.000:0,0,0 0|0:0.200:0,0,0 0|0:0.200:0,0,0 0|0:0.250:0,0,0 0|0:0.300:0,0,0 0|0:0.250:0,0,0 0|0:0.050:0,0,0 0|0:0.150:0,0,0 0|0:0.200:0,0,0 0|0:0.250:0,0,0 0|0:0.350:0,0,0 0|0:0.450:0,0,0 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.250:0,0,0 0|0:0.150:0,0,0 0|0:0.050:0.00,-0.60,-6.20 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.300:0,0,0 0|0:0.050:0.00,-0.90,-11.90 0|0:0.100:0.00,-0.30,-3.90 0|0:0.200:0,0,0 0|0:0.350:0,0,0 0|0:0.250:0,0,0 0|0:0.100:0,0,0 0|0:0.050:0,0,0 0|0:0.250:0.00,-0.30,-4.10 0|0:0.050:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.300:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0.00,-0.30,-4.10 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.300:0,0,0 0|0:0.350:0,0,0 0|0:0.450:0,0,0 0|0:0.200:0,0,0 0|0:0.300:0,0,0 0|0:0.300:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.200:0,0,0 0|0:0.150:0,0,0 0|0:0.250:0,0,0 0|0:0.350:0,0,0 0|0:0.000:0.00,-0.90,-12.20 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.200:0,0,0 0|0:0.200:0,0,0 0|0:0.200:0,0,0 0|0:0.050:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0
1 13980 rs151276478 T . 100 PASS AA=.;AC=0;AF=0.02;AFR_AF=0.01;AMR_AF=0.02;AN=170;ASN_AF=0.02;AVGPOST=0.9221;ERATE=0.0034;EUR_AF=0.02;LDAF=0.0525;RSQ=0.3603;SNPSOURCE=LOWCOV;THETA=0.0139;VT=SNP GT:DS:GL 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.100:-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 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.45,-0.46,-0.52 0|0:0.050:-0.25,-0.43,-1.13 0|0:0.000:-0.07,-0.81,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.03,-1.12,-5.00 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.100:-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 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.000:-0.11,-0.67,-2.93 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.250:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.100:-0.477139,-0.477113,-0.477113 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.19,-0.47,-1.85 0|0:0.000:-0.04,-1.06,-5.00 0|0:0.200:-0.24,-0.45,-1.18 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.250:-0.48,-0.48,-0.48 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.000:-0.0404435,-1.051,-5 0|0:0.000:-0.34,-0.41,-0.81 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.200:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.19,-0.45,-2.25 0|0:0.000:-0.04,-1.06,-5.00 0|0:0.150:-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 0|0:0.250:-0.477139,-0.477113,-0.477113 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.000:-0.08,-0.78,-5.00 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.100:-0.48,-0.48,-0.48 0|0:0.250:-0.48,-0.48,-0.48 0|0:0.300:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.150:-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 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.050:-0.11,-0.66,-2.80 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.25,-0.44,-1.12 0|0:0.000:-0.48,-0.48,-0.48 0|0:0.000:-0.00278841,-2.19382,-5 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.150:-0.48,-0.48,-0.48 0|0:0.150:-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 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 AA=T;AC=122;AF=0.73;AFR_AF=0.48;AMR_AF=0.80;AN=170;ASN_AF=0.89;AVGPOST=0.7335;ERATE=0.0183;EUR_AF=0.73;LDAF=0.6576;RSQ=0.5481;SNPSOURCE=LOWCOV;THETA=0.0162;VT=SNP GT:DS:GL 1|1:1.500:-5.00,-0.67,-0.10 1|1:1.800:-5.00,-0.66,-0.11 0|1:0.800:-0.19,-0.45,-2.24 1|1:1.550:-0.48,-0.48,-0.48 1|0:0.650:-0.13,-0.61,-2.25 1|1:1.550:-0.48,-0.48,-0.48 1|1:1.550:-0.48,-0.48,-0.48 1|0:1.050:-0.48,-0.48,-0.48 0|1:1.100:-0.20,-0.47,-1.42 1|1:1.400:-0.48,-0.48,-0.48 0|0:0.500:-0.17,-0.51,-1.66 1|1:1.500:-0.48,-0.48,-0.48 1|0:0.800:-0.23,-0.44,-1.26 1|0:1.000:-1.14,-0.03,-4.22 0|0:0.200:-0.02,-1.35,-5.00 1|0:0.800:-0.54,-0.15,-5.00 1|1:1.400:-0.48,-0.48,-0.48 0|1:1.000:-1.63,-0.01,-4.40 1|1:1.350:-0.48,-0.48,-0.48 1|1:1.550:-0.48,-0.48,-0.48 1|1:1.450:-0.48,-0.48,-0.48 1|1:1.450:-0.48,-0.48,-0.48 1|1:1.350:-0.48,-0.48,-0.48 1|1:1.700:-0.48,-0.48,-0.48 1|1:1.500:-0.48,-0.48,-0.48 1|1:1.350:-0.48,-0.48,-0.48 0|1:0.850:-0.19,-0.49,-1.59 0|0:0.450:-0.07,-0.81,-3.66 1|1:1.750:-5.00,-0.58,-0.13 0|0:0.650:-0.13,-0.59,-2.08 0|0:0.000:-0.00,-2.30,-5.00 1|0:0.700:-0.21,-0.47,-1.41 0|0:0.350:-0.11,-0.64,-2.72 1|1:1.350:-0.48,-0.48,-0.48 1|1:1.500:-0.40,-0.45,-0.61 1|1:1.200:-0.48,-0.48,-0.48 1|1:1.200:-0.374811,-0.424928,-0.694176 0|1:1.000:-1.81,-0.01,-5.00 0|1:0.900:-0.20,-0.48,-1.47 1|1:1.450:-0.48,-0.48,-0.48 0|1:1.000:-5.00,-0.00,-2.84 1|1:1.250:-0.48,-0.48,-0.48 1|1:1.350:-0.48,-0.48,-0.48 1|1:1.800:-5.00,-0.86,-0.06 1|1:1.900:-4.70,-0.66,-0.11 1|1:1.600:-0.477139,-0.477113,-0.477113 1|1:1.500:-0.48,-0.48,-0.48 0|1:1.200:-0.48,-0.48,-0.48 1|1:1.750:-0.48,-0.48,-0.48 1|1:1.750:-2.81,-0.45,-0.19 1|1:1.150:-0.48,-0.48,-0.48 1|1:1.800:-3.18,-0.47,-0.18 1|1:1.550:-2.59,-0.46,-0.19 1|1:1.550:-0.48,-0.48,-0.48 0|0:0.650:-0.06,-0.86,-5.00 1|1:1.600:-0.48,-0.48,-0.48 1|1:1.700:-2.45593,-0.438493,-0.199173 1|1:1.600:-0.48,-0.48,-0.48 0|0:0.300:-0.07,-0.82,-3.80 1|1:1.600:-2.35,-0.44,-0.20 0|0:0.100:-0.02,-1.29,-5.00 0|1:1.100:-0.34,-0.41,-0.82 1|1:1.850:-5.00,-0.89,-0.06 1|1:1.650:-2.41,-0.46,-0.19 1|1:1.300:-0.48,-0.48,-0.48 1|1:1.300:-0.48,-0.48,-0.48 0|1:1.350:-0.48,-0.48,-0.48 1|1:1.600:-0.48,-0.48,-0.48 0|0:0.700:-0.17,-0.50,-2.56 1|1:1.350:-0.48,-0.48,-0.48 1|1:1.850:-2.58,-0.46,-0.19 0|0:0.950:-0.29,-0.40,-1.01 1|0:1.200:-0.28,-0.43,-0.99 1|0:0.950:-0.33,-0.43,-0.80 1|0:0.850:-0.24,-0.44,-1.18 1|1:1.500:-0.48,-0.48,-0.48 0|1:0.650:-0.0794071,-0.777024,-5 1|1:1.500:-0.48,-0.48,-0.48 0|1:1.250:-0.48,-0.48,-0.48 0|1:1.150:-0.48,-0.48,-0.48 1|0:0.750:-0.27,-0.44,-1.01 0|1:0.750:-0.12,-0.62,-2.49 0|0:0.500:-0.17,-0.51,-1.69 1|1:1.450:-0.48,-0.48,-0.48 1|1:1.600:-0.48,-0.48,-0.48
1 46402 rs199681827 C . 31 PASS AA=.;AC=0;AF=0.0037;AFR_AF=0.01;AN=170;ASN_AF=0.0017;AVGPOST=0.8325;ERATE=0.0072;LDAF=0.0903;RSQ=0.0960;THETA=0.0121;VT=INDEL GT:DS:GL 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0.00,-0.60,-8.30 0|0:0.100:0,0,0 0|0:0.250:0,0,0 0|0:0.150:0,0,0 0|0:0.500:-0.80,-0.20,0.00 0|0:0.200:0,0,0 0|0:0.250:0,0,0 0|0:0.200:0,0,0 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.300:0,0,0 0|0:0.200:0,0,0 0|0:0.450:0,0,0 0|0:0.400:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.200:0,0,0 0|0:0.250:0,0,0 0|0:0.200:0,0,0 0|0:0.300:0,0,0 0|0:0.300:0,0,0 0|0:0.150:0,0,0 0|0:0.250:0,0,0 0|0:0.200:0,0,0 0|0:0.300:0,0,0 0|0:0.150:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.300:0,0,0 0|0:0.550:0,0,0 0|0:0.250:0,0,0 0|0:0.300:0,0,0 0|0:0.250:0,0,0 0|0:0.400:0,0,0 0|0:0.250:0,0,0 0|0:0.250:0,0,0 0|0:0.350:0,0,0 0|0:0.050:0,0,0 0|0:0.150:0.00,-0.30,-5.20 0|0:0.300:0,0,0 0|0:0.200:0,0,0 0|0:0.050:0,0,0 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.250:0,0,0 0|0:0.250:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.250:0,0,0 0|0:0.150:0,0,0 0|0:0.250:0,0,0 0|0:0.000:0.00,-0.30,-5.20 0|0:0.150:0,0,0 0|0:0.400:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.250:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.300:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.300:0,0,0 0|0:0.100:0,0,0 0|0:0.550:0,0,0 0|0:0.200:0,0,0 0|0:0.400:0,0,0 0|0:0.100:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0
1 47190 rs200430748 G . 192 PASS AA=G;AC=0;AF=0.01;AFR_AF=0.06;AMR_AF=0.0028;AN=170;AVGPOST=0.9041;ERATE=0.0041;LDAF=0.0628;RSQ=0.2883;THETA=0.0153;VT=INDEL GT:DS:GL 0|0:0.300:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0,0,0 0|0:0.050:0,0,0 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0.00,-0.30,-3.60 0|0:0.150:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0,0,0 0|0:0.000:0,0,0 0|0:0.150:0.00,-0.30,-3.60 0|0:0.050:0.00,-0.30,-3.60 0|0:0.100:0,0,0 0|0:0.100:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0.00,-0.30,-3.60 0|0:0.100:0,0,0 0|0:0.050:0.00,-0.60,-7.20 0|0:0.200:0,0,0 0|0:0.200:0,0,0 0|0:0.000:0,0,0 0|0:0.200:0,0,0 0|0:0.200:0,0,0 0|0:0.300:0,0,0 0|0:0.000:0.00,-0.30,-3.60 0|0:0.050:0.00,-0.30,-3.60 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0.00,-0.30,-3.60 0|0:0.000:0,0,0 0|0:0.050:0.00,-0.30,-3.60 0|0:0.000:0,0,0 0|0:0.050:0,0,0 0|0:0.250:0,0,0 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.150:0.00,-0.30,-3.60 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.100:0.00,-0.30,-3.60 0|0:0.100:0,0,0 0|0:0.050:0,0,0 0|0:0.100:0,0,0 0|0:0.200:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0,0,0 0|0:0.150:0,0,0 0|0:0.050:0.00,-0.30,-3.60 0|0:0.100:0,0,0 0|0:0.100:0.00,-0.30,-3.60 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.000:0.00,-0.30,-3.60 0|0:0.150:0,0,0 0|0:0.550:0,0,0 0|0:0.000:0,0,0 0|0:0.150:0,0,0 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0,0,0 0|0:0.150:0,0,0 0|0:0.000:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.000:0.00,-0.30,-2.80 0|0:0.050:0,0,0 0|0:0.200:0,0,0 0|0:0.000:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 0|0:0.000:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 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 0|0:0.050:0.00,-0.30,-3.60
|