##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.2-145-gab561e1+htslib-1.2.1-177-g4494fa6
##samtoolsCommand=samtools mpileup -u -f ref.fa S1.bam S2.bam S3.bam S4.bam
##reference=file://ref.fa
##contig=<ID=rotavirus,length=1074>
##ALT=<ID=X,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##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=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##bcftools_callVersion=1.2-108-gd4d42ca+htslib-1.2.1-177-g4494fa6
##bcftools_callCommand=call -c -v -O z -o mutations.vcf.gz -
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4
rotavirus	51	.	A	G	22.5544	.	DP=944;VDB=3.53678e-05;SGB=-61.9012;RPB=0.993129;MQB=1;BQB=1;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=849,0,93,0;MQ=60;FQ=23.7972;PV4=1,1,1,1	GT:PL	0/0:0,255,134	0/0:0,255,127	0/0:0,255,137	1/1:70,255,0
rotavirus	91	.	A	T	5.44937	.	DP=1359;VDB=0.313337;SGB=-369.163;RPB=0.0393173;MQB=1;BQB=0.951201;MQ0F=0;AF1=0.124963;AC1=1;DP4=1134,0,225,0;MQ=60;FQ=5.8713;PV4=1,4.80825e-05,1,1	GT:PL	0/0:0,255,133	0/1:40,0,31	0/0:0,255,134	0/0:0,255,82
rotavirus	130	.	T	C	4.11916	.	DP=1349;VDB=0.00084636;SGB=-335.275;RPB=0.762964;MQB=1;BQB=1;MQ0F=0;AF1=0.124933;AC1=1;DP4=1139,0,204,0;MQ=60;FQ=4.48321;PV4=1,1,1,1	GT:PL	0/1:38,0,35	0/0:0,255,132	0/0:0,255,132	0/0:0,255,79
rotavirus	232	.	T	A	5.44927	.	DP=1308;VDB=0.0100544;SGB=-340.116;RPB=0.453119;MQB=1;BQB=1;MQ0F=0;AF1=0.124959;AC1=1;DP4=1098,0,207,0;MQ=60;FQ=5.87117;PV4=1,1,1,1	GT:PL	0/1:40,0,35	0/0:0,255,135	0/0:0,255,132	0/0:0,255,81
rotavirus	267	.	C	G	4.75869	.	DP=1393;VDB=0.367507;SGB=-383.686;RPB=0.0284076;MQB=1;BQB=0.953186;MQ0F=0;AF1=0.124951;AC1=1;DP4=1156,0,234,0;MQ=60;FQ=5.15288;PV4=1,5.65123e-05,1,1	GT:PL	0/1:39,0,32	0/0:0,255,132	0/0:0,255,136	0/0:0,255,76
rotavirus	424	.	A	G	52.9919	.	DP=1555;VDB=0.000623759;SGB=-160.094;RPB=0.0600948;MQB=1;MQSB=1;BQB=0.956333;MQ0F=0;AF1=0.125;AC1=1;DP4=1096,206,198,55;MQ=60;FQ=53.5713;PV4=0.0270045,4.0796e-05,1,1	GT:PL	0/0:0,255,200	0/1:89,0,51	0/0:0,255,189	0/0:0,255,153
rotavirus	520	.	T	A	53.9919	.	DP=2372;VDB=0.730588;SGB=-738.702;RPB=0.805995;MQB=1;MQSB=1;BQB=0.215002;MQ0F=0;AF1=0.125;AC1=1;DP4=1055,856,223,231;MQ=60;FQ=54.5713;PV4=0.0211343,5.03431e-23,1,1	GT:PL	0/0:0,255,231	0/0:0,255,225	0/1:90,0,112	0/0:0,255,204
rotavirus	536	.	A	T	999	.	DP=2442;VDB=0.0230995;SGB=-980.758;RPB=0.988415;MQB=1;MQSB=1;BQB=0.656787;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=923,915,331,273;MQ=60;FQ=999;PV4=0.0543741,1.08393e-11,1,1	GT:PL	1/1:228,255,0	0/0:0,255,232	0/0:0,255,230	0/0:0,255,213
rotavirus	562	.	A	G	65.9921	.	DP=2552;VDB=0.911719;SGB=-257.817;RPB=0.706529;MQB=1;MQSB=1;BQB=0.0219678;MQ0F=0;AF1=0.125;AC1=1;DP4=1148,1246,80,76;MQ=60;FQ=66.5714;PV4=0.456934,0,1,0.264263	GT:PL	0/0:0,255,225	0/0:0,255,242	0/0:0,255,228	0/1:102,0,110
rotavirus	583	.	G	C	72.9921	.	DP=2395;VDB=0.959181;SGB=-240.067;RPB=0.450296;MQB=1;MQSB=1;BQB=0.784385;MQ0F=0;AF1=0.125;AC1=1;DP4=1000,1249,69,76;MQ=60;FQ=73.5715;PV4=0.490957,3.2323e-19,1,0.118979	GT:PL	0/0:0,255,238	0/0:0,255,236	0/0:0,255,239	0/1:109,0,115
rotavirus	661	.	T	A	94.9924	.	DP=1575;VDB=0.175801;SGB=-451.462;RPB=0.267008;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.125;AC1=1;DP4=197,1101,39,237;MQ=60;FQ=95.5718;PV4=0.710857,1,1,1	GT:PL	0/0:0,255,255	0/1:131,0,118	0/0:0,255,255	0/0:0,255,212
rotavirus	693	.	T	G	999	.	DP=1445;VDB=0.954618;SGB=-287.745;RPB=0.351895;MQB=1;MQSB=1;BQB=0.835813;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=49,935,36,425;MQ=60;FQ=999;PV4=0.0408935,5.22426e-06,1,0.00476177	GT:PL	1/1:255,255,0	0/0:0,255,255	0/0:0,255,255	0/0:0,255,184
rotavirus	738	.	T	A	32.9939	.	DP=1379;VDB=0.660291;SGB=-430.484;RPB=0.955052;MQB=1;MQSB=1;BQB=0.970112;MQ0F=0;AF1=0.125003;AC1=1;DP4=8,1094,8,255;MQ=60;FQ=33.573;PV4=0.0052528,0.04768,1,1	GT:PL	0/0:0,255,131	0/0:0,255,221	0/1:69,0,35	0/0:0,255,127
rotavirus	799	.	A	C	89.5311	.	DP=1247;VDB=0.279467;SGB=-69.3156;RPB=0.621805;MQB=1;BQB=0.134372;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=0,773,0,474;MQ=60;FQ=90.7799;PV4=1,1.06203e-13,1,1	GT:PL	0/0:0,255,132	0/0:0,255,133	1/1:137,255,0	0/0:0,255,80
rotavirus	812	.	G	T	87.5311	.	DP=1269;VDB=0.857678;SGB=-71.5897;RPB=0.420813;MQB=1;BQB=0.999215;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=0,755,0,494;MQ=60;FQ=88.7799;PV4=1,1,1,0.0437171	GT:PL	0/0:0,255,131	0/0:0,255,137	1/1:135,255,0	0/0:0,255,83
rotavirus	833	.	G	A	91.5311	.	DP=1276;VDB=0.169138;SGB=-538.602;RPB=0.145223;MQB=1;BQB=0.970198;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=0,940,0,330;MQ=60;FQ=92.78;PV4=1,0.00170144,1,1	GT:PL	1/1:139,255,0	0/0:0,255,127	0/0:0,255,134	0/0:0,255,89
rotavirus	916	.	A	T	83.531	.	DP=1319;VDB=1.18635e-05;SGB=-506.328;RPB=0.155593;MQB=1;BQB=1;MQ0F=0;AF1=0.25;G3=0.75,0,0.25;HWE=0.033921;AC1=2;DP4=0,985,0,310;MQ=60;FQ=84.7799;PV4=1,1,1,1	GT:PL	1/1:131,255,0	0/0:0,255,129	0/0:0,255,135	0/0:0,255,80
rotavirus	946	.	C	A	4.75877	.	DP=1371;VDB=0.728947;SGB=-391.755;RPB=0.773259;MQB=1;BQB=1;MQ0F=0;AF1=0.124954;AC1=1;DP4=0,1132,0,239;MQ=60;FQ=5.15297;PV4=1,1,1,1	GT:PL	0/0:0,255,129	0/1:39,0,30	0/0:0,255,132	0/0:0,255,74
rotavirus	961	.	T	A	4.75867	.	DP=1345;VDB=0.902083;SGB=-327.207;RPB=0.145671;MQB=1;BQB=0.793711;MQ0F=0;AF1=0.124949;AC1=1;DP4=0,1146,0,199;MQ=60;FQ=5.15285;PV4=1,1.56767e-09,1,0.127045	GT:PL	0/1:39,0,33	0/0:0,255,130	0/0:0,255,130	0/0:0,255,74
rotavirus	1044	.	A	T	59.5307	.	DP=689;VDB=1.67785e-30;SGB=72.9125;RPB=0.98876;MQB=1;BQB=0.992141;MQ0F=0;AF1=0.25;G3=0.75,8.80576e-42,0.25;HWE=0.033921;AC1=2;DP4=0,491,0,198;MQ=60;FQ=60.7796;PV4=1,1,1,1	GT:PL	0/0:0,255,102	1/1:107,255,0	0/0:0,255,130	0/0:0,199,67
rotavirus	1045	.	C	G	57.5307	.	DP=665;VDB=1.30405e-41;SGB=-362.708;RPB=0.999761;MQB=1;BQB=0.748568;MQ0F=0;AF1=0.25;G3=0.75,2.21171e-36,0.25;HWE=0.033921;AC1=2;DP4=0,444,0,221;MQ=60;FQ=58.7795;PV4=1,2.55278e-05,1,0.428504	GT:PL	0/0:0,255,106	0/0:0,255,107	1/1:105,255,0	0/0:0,172,63
rotavirus	1054	.	C	G	15.65	.	DP=487;VDB=1.4013e-45;SGB=42.7815;RPB=0.95941;MQB=1;BQB=1;MQ0F=0;AF1=0.249999;G3=0.75,2.21169e-28,0.25;HWE=0.0339211;AC1=2;DP4=0,364,0,120;MQ=60;FQ=16.8692;PV4=1,1,1,1	GT:PL	0/0:0,255,90	1/1:63,235,0	0/0:0,255,99	0/0:0,132,66
rotavirus	1064	.	G	A	21.5606	.	DP=250;VDB=2.70971e-16;SGB=8.40135;RPB=0.935144;MQB=1;BQB=0.683886;MQ0F=0;AF1=0.25;G3=0.75,2.37734e-17,0.25;HWE=0.033921;AC1=2;DP4=0,219,0,31;MQ=60;FQ=22.8019;PV4=1,1.22605e-06,1,1	GT:PL	0/0:0,244,70	0/0:0,199,65	0/0:0,217,68	1/1:69,84,0