|
0
|
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 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00002
|
|
|
33 20 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=2;AC=1 GT:PL:DP:GQ 0/1:140,0,255:71:99
|
|
|
34 20 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=2;AC=1 GT:PL:DP:GQ 0/1:192,0,255:82:99
|
|
|
35 20 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=2;AC=1 GT:PL:DP:GQ 0|1:192,0,255:13:99
|
|
|
36 X 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=1;AC=1 GT:PL:DP:GQ 1:255,0:33:99
|
|
|
37 X 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=1;AC=1 GT:PL:DP:GQ 1:255,0:33:99
|
|
|
38 Y 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=1;AC=1 GT:PL:DP:GQ 1:255,0:64:99
|
|
|
39 Y 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=1;AC=1 GT:PL:DP:GQ 1:95,0:130:99
|
