1##fileformat=VCFv4.1 2##FILTER=<ID=PASS,Description="All filters passed"> 3##reference=file:///seq/references/1000Genomes-NCBI37.fasta 4##contig=<ID=11,length=135006516> 5##contig=<ID=20,length=63025520> 6##contig=<ID=X,length=155270560> 7##contig=<ID=Y,length=59373566> 8##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> 9##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> 10##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions"> 11##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> 12##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction"> 13##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)"> 14##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F"> 15##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 16##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads"> 17##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> 18##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads"> 19##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> 20##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth"> 21##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> 22##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> 23##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> 24##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 25##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 26##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> 27##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]"> 28##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]"> 29##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]"> 30##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]"> 31##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]"> 32##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> 33##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency"> 34##INFO=<ID=MAF,Number=1,Type=Float,Description="Frequency of the second most common allele"> 35#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 3611 2343543 . A . 999 PASS DP=100223;NS=3;AN=6 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99 3711 5464562 . C T 999 PASS DP=0;NS=0;AN=0;AF=.;MAF=.;AC=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:. 3820 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;NS=3;AN=6;AF=0.833333;MAF=0.166667;AC=5 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99 3920 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;NS=3;AF=0.666667;MAF=0.333333 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0 4020 138125 rs2298108 G T 999 PASS DP4=174391,20849,82080,4950;DP=286107;Dels=0;FS=3200;HWE=0.199462;ICF=0.01858;MQ0=0;MQ=46;PV4=0,0,0,1;QD=17.22;AN=6;AC=4;NS=3;AF=0.666667;MAF=0.333333 GT:PL:DP:GQ 0/1:135,0,163:66:99 0/1:140,0,255:71:99 1/1:255,199,0:66:99 4120 138148 rs2298109 C T 999 PASS DP4=194136,45753,94945,14367;DP=356657;Dels=0;FS=3200;HWE=0.177865;ICF=0.0198;MQ0=0;MQ=47;PV4=0,0,0,1;QD=14.57;AN=6;AC=4;NS=3;AF=0.666667;MAF=0.333333 GT:PL:DP:GQ 0/1:195,0,255:87:99 0/1:192,0,255:82:99 1/1:255,235,0:78:99 4220 271225 . T TTTA,TA 999 StrandBias DP4=29281,42401,27887,29245;DP=272732;INDEL;IS=95,0.748031;MQ=47;PV4=0,1,0,1;QD=0.0948;AN=6;AC=2,2;NS=3;AF=0.333333,0.333333;MAF=0.333333 GT:DP:GQ:PL 0/2:33:49:151,53,203,0,52,159 0/1:51:99:255,0,213,255,255,255 1/2:47:99:255,255,255,255,0,241 4320 304568 . C T 999 PASS DP4=16413,4543,945,156;DP=43557;Dels=0;FS=3200;HWE=0.076855;ICF=0.0213;MQ0=0;MQ=50;PV4=0,0,0,1;QD=15.45;AN=6;AC=4;NS=3;AF=0.666667;MAF=0.333333 GT:PL:DP:GQ 0|1:95,0,255:90:99 0|1:192,0,255:13:99 1|1:255,95,0:60:99 4420 326891 . A AC 999 PASS DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2;NS=2;AF=0.5;MAF=0.5 GT:DP:GQ:PL 0|1:117:99:255,0,132 0|1:111:99:255,0,139 ./.:.:.:.,.,. 45X 2928329 rs62584840 C T 999 PASS DP4=302,9137,32,1329;DP=11020;Dels=0;FS=13.38;HWE=0.284332;ICF=0.0253;MQ0=0;MQ=49;PV4=0.094,0,0,1;QD=18.61;AN=4;AC=1;NS=3;AF=0.25;MAF=0.25 GT:PL:DP:GQ 0:0,56:2:73 0:0,81:3:98 0/1:73,0,19:4:30 46X 2933066 rs61746890 G C 999 PASS DP4=69865,100561,461,783;DP=173729;Dels=0;FS=10.833;MQ0=0;MQ=50;PV4=0.005,3.6e-14,0,1;QD=15.33;AN=4;AC=1;NS=3;AF=0.25;MAF=0.25 GT:PL:DP:GQ 0:0,255:39:99 0:0,255:37:99 0/1:255,255,255:62:99 47X 2942109 rs5939407 T C 999 PASS DP4=23273,27816,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3;NS=3;AF=0.75;MAF=0.25 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 1/1:255,157,0:52:99 48X 3048719 . T C 999 PASS DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=2;NS=3;AF=0.5;MAF=0.5 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 0|1:255,0,157:52:99 49Y 8657215 . C A 999 PASS DP4=74915,114274,1948,2955;DP=195469;Dels=0;FS=3.181;MQ0=0;MQ=50;PV4=0.86,1,0,1;QD=33.77;AN=2;AC=1;NS=2;AF=0.5;MAF=0.5 GT:PL:DP:GQ 0:0,255:47:99 1:255,0:64:99 .:.:.:. 50Y 10011673 rs78249411 G A 999 MinAB DP4=47351,30839,178796,279653;DP=550762;Dels=0;FS=41.028;MQ0=37362;MQ=26;PV4=0,0,0,1;QD=17.45;AN=2;AC=2;NS=2;AF=1;MAF=0 GT:PL:DP:GQ 1:126,101:146:37 1:95,0:130:99 .:.:.:. 51