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##fileformat=VCFv4.1
##samtoolsVersion=0.1.14 (r933:170)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=RP,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=.,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
##INFO=<ID=RS,Number=1,Type=String,Description="rs ID">
##INFO=<ID=GeneID,Number=1,Type=String,Description="Ensembl Gene ID">
##INFO=<ID=Effect,Number=1,Type=String,Description="Effect of variation on transcript">
##source_20110231.1=/home/gobyweb/bin/vcf-annotate -a /scratchLocal/gobyweb/input-data/reference-db/1000GENOMES.37/homo_sapiens/reference//var-annotations-sorted.tsv.gz -d descriptions.lst -c CHROM,FR OM,INFO/RS,INFO/GeneID,INFO/Effect
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT QMMNMJW.bam PIAXRTU.bam
1 145497099 . A G 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
10 94234 . TAA TAAA 33.5 . INDEL;DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-38.3;QCHI2=1;PCHI2=0.749;PC2=3,3 GT:PL:GQ 1/1:37,3,0:42 1/1:37,3,0:42
10 114158 . A G 17.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-30.8;QCHI2=1;PCHI2=0.752;PC2=3,3 GT:PL:GQ 1/1:25,3,0:42 1/1:25,3,0:42
10 123469 . A G 3.61 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-30.7;QCHI2=1;PCHI2=0.85;PC2=3,3 GT:PL:GQ 1/1:17,3,0:42 1/1:17,3,0:42
10 181146 . A G 3.61 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.85;PC2=3,3 GT:PL:GQ 1/1:17,3,0:42 1/1:17,3,0:42
10 181486 . G A 15.5 . DP=4;AF1=0.5024;CI95=0.5,0.5;DP4=2,0,2,0;MQ=32;FQ=7.07;QCHI2=0;PCHI2=0.984;PC2=3,3;PV4=1,0,1,1 GT:PL:GQ 0/1:25,0,19:21 0/1:25,0,19:21
10 181567 . C G 19.1 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.8;QCHI2=1;PCHI2=0.75;PC2=3,3 GT:PL:GQ 1/1:26,3,0:42 1/1:26,3,0:42
10 182055 . A C 5.04 . DP=4;AF1=0.4976;CI95=0.5,0.5;DP4=2,0,2,0;MQ=37;FQ=7.07;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,0,1,1 GT:PL:GQ 0/1:19,0,25:21 0/1:19,0,25:21
10 182057 . C A 6.51 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=37;FQ=6.51;QCHI2=0;PCHI2=0.978;PC2=3,3;PV4=1,1,1,0 GT:PL:GQ 0/1:20,0,20:20 0/1:20,0,20:20
10 182271 . C A 3.79 . DP=6;AF1=0.496;CI95=0.25,0.5;DP4=4,0,2,0;MQ=37;FQ=5.73;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,4.5e-05,1,0.31 GT:PL:GQ 0/1:18,0,59:21 0/1:18,0,59:21
10 182801 . G C 3.79 . DP=4;AF1=0.4962;CI95=0.25,0.5;DP4=2,0,2,0;MQ=37;FQ=5.73;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,0,1,1 GT:PL:GQ 0/1:18,0,31:21 0/1:18,0,31:21
10 183183 . T G 11.4 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.763;PC2=3,3 GT:PL:GQ 1/1:22,3,0:42 1/1:22,3,0:42
10 185358 . C T 3.61 . DP=2;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-30.7;QCHI2=1;PCHI2=0.85;PC2=3,3 GT:PL:GQ 1/1:17,3,0:42 1/1:17,3,0:42
10 186159 . T C 9.8 . DP=10;AF1=0.4984;CI95=0.5,0.5;DP4=8,0,2,0;MQ=37;FQ=12.6;QCHI2=0;PCHI2=0.987;PC2=3,3;PV4=1,0.0027,1,1 GT:PL:GQ 0/1:22,0,100:25 0/1:22,0,100:25
10 188262 . A T 3.79 . DP=4;AF1=0.4962;CI95=0.25,0.5;DP4=2,0,2,0;MQ=37;FQ=5.73;QCHI2=0;PCHI2=0.98;PC2=3,3;PV4=1,0,1,1 GT:PL:GQ 0/1:18,0,31:21 0/1:18,0,31:21
10 188345 . T C 9.8 . DP=6;AF1=0.4984;CI95=0.5,0.5;DP4=4,0,2,0;MQ=33;FQ=12.6;QCHI2=0;PCHI2=0.987;PC2=3,3;PV4=1,0.00056,1,1 GT:PL:GQ 0/1:22,0,49:25 0/1:22,0,49:25
10 189046 . G T 17.4 . DP=6;AF1=0.4994;CI95=0.5,0.5;DP4=4,0,2,0;MQ=37;FQ=20.3;QCHI2=0;PCHI2=0.994;PC2=3,3;PV4=1,0.00031,1,1 GT:PL:GQ 0/1:26,0,59:29 0/1:26,0,59:29
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