annotate test-data/freebayes-phix174.gvcf @ 40:0d8581534009 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 48700fed491e8056cddd1ee7d8bc9ca08e19fe8d

##fileformat=VCFv4.2
##fileDate=20250805
##source=freeBayes v1.3.10
##reference=localref.fa
##contig=<ID=phiX174,length=5386>
##phasing=none
##commandline="freebayes --region phiX174:0..5386 -f freebayes-phix174.fasta freebayes-phix174.bam --gvcf"
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Float,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Float,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
phiX174	1	.	G	<*>	0	.	DP=4;END=310;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	86804:4:0:87601:4:797:0
phiX174	311	.	A	G	0.00392026	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=7.0097;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:478:2:70:-1.91487,0,-18.7749
phiX174	312	.	T	<*>	0	.	DP=8;END=373;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	31465:8:5:31945:8:480:0
phiX174	374	.	T	G	23.3387	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:2,2:2:141:2:75:-5.19433,0,-3.54586
phiX174	375	.	A	<*>	0	.	DP=6;END=912;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	227000:6:0:229264:6:2264:0
phiX174	913	.	A	C	2.27318	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=0.380296;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5:3,2:3:171:2:67:-3.54411,0,-6.47921
phiX174	914	.	G	<*>	0	.	DP=7;END=1204;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	129636:7:0:130843:7:1207:0
phiX174	1205	.	A	C	0.00388031	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=7.01995;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:456:2:67:-2.11454,0,-21.3383
phiX174	1206	.	C	<*>	0	.	DP=9;END=1244;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	20203:9:0:20483:8:280:0
phiX174	1245	.	G	T	0.0324554	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=4.8927;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:389:2:70:-2.83427,0,-14.5618
phiX174	1246	.	G	<*>	0	.	DP=9;END=1248;MIN_DP=9	GQ:DP:MIN_DP:QR:RO:QA:AO	1576:9:9:1576:9:0:0
phiX174	1249	.	T	G	0.0166698	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=5.56079;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:464:2:74:-1.94207,0,-16.5662
phiX174	1250	.	A	<*>	0	.	DP=9;END=1444;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	117232:9:0:118408:9:1176:0
phiX174	1445	.	C	A	0.147157	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=3.36782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:5,2:5:273:2:76:-2.52649,0,-12.4911
phiX174	1446	.	C	<*>	0	.	DP=5;END=1576;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	40596:5:1:41046:5:450:0
phiX174	1577	.	A	C	0.0123232	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=5.8634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:7,2:7:460:2:60:-1.81064,0,-19.8257
phiX174	1578	.	T	<*>	0	.	DP=11;END=1630;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	37187:11:0:37576:11:389:0
phiX174	1631	.	T	G	0.00100612	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=8.3701;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:500:2:68:-1.52818,0,-17.3788
phiX174	1632	.	A	<*>	0	.	DP=10;END=1664;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	21423:10:0:21616:10:193:0
phiX174	1665	.	C	A	0.0164128	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=5.57635;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:9,2:9:587:2:65:-2.35331,0,-21.269
phiX174	1666	.	A	<*>	0	.	DP=10;END=1771;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	62611:10:4:63430:9:819:0
phiX174	1772	.	T	G	0.0180574	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=5.48067;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:7,2:7:425:2:59:-1.97686,0,-17.3816
phiX174	1773	.	T	<*>	0	.	DP=11;END=1785;MIN_DP=9	GQ:DP:MIN_DP:QR:RO:QA:AO	8476:11:9:8574:11:98:0
phiX174	1786	.	T	G	7.94817e-05	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.9085;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:10,2:10:537:2:59:-0.861483,0,-25.1364
phiX174	1787	.	G	<*>	0	.	DP=4;END=1944;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	47842:4:1:48427:4:585:0
phiX174	1945	.	T	G	1.01422	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.3354;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:263:2:59:-3.25425,0,-11.8637
phiX174	1946	.	G	<*>	0	.	DP=6;END=2229;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	106303:6:0:107388:5:1085:0
phiX174	2230	.	T	G	0.00580188	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=6.61746;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:491:2:80:-2.28934,0,-22.3591
phiX174	2231	.	G	<*>	0	.	DP=5;END=2698;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	166680:5:1:168664:5:1984:0
phiX174	2699	.	C	A	2.04855	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=0.517362;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:2,2:2:109:2:76:-3.4054,0,-5.58455
phiX174	2700	.	C	<*>	0	.	DP=3;END=2721;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	5193:3:2:5224:3:31:0
phiX174	2722	.	T	G	1.01772	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.33197;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5:3,2:3:150:2:67:-3.1308,0,-7.62253
phiX174	2723	.	A	<*>	0	.	DP=5;END=2813;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	29653:5:0:29924:5:271:0
phiX174	2814	.	T	G	0.670623	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.79322;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=135;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=9.52472;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5:3,2:3:135:2:57:-2.93048,0,-6.73807
phiX174	2815	.	T	<*>	0	.	DP=7;END=2827;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	5398:7:5:5428:6:30:0
phiX174	2828	.	T	G	0.160629	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31;NS=1;NUMALT=1;ODDS=3.27866;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPL=0;RPP=7.35324;RPPR=4.45795;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:6,2:6:348:2:100:-3.34336,0,-13.6819
phiX174	2829	.	G	<*>	0	.	DP=4;END=2982;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	44584:4:0:45208:4:624:0
phiX174	2983	.	T	G	1.55467	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=0.843116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5:3,2:3:150:2:57:-3.34311,0,-7.61298
phiX174	2984	.	G	<*>	0	.	DP=5;END=3109;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	40846:5:0:41267:5:421:0
phiX174	3110	.	T	C	1.16857	.	AB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=1.17522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:6,3:6:361:3:94:-4.02963,0,-16.4039
phiX174	3111	.	G	<*>	0	.	DP=7;END=3154;MIN_DP=5	GQ:DP:MIN_DP:QR:RO:QA:AO	20734:7:5:20914:7:180:0
phiX174	3155	.	T	G	5.42491	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=0.911202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:5,2:5:299:2:75:-4.38484,0,-11.5688
phiX174	3156	.	A	<*>	0	.	DP=11;END=3183;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	19187:11:0:19362:10:175:0
phiX174	3184	.	A	C	0.000128182	.	AB=0.153846;ABP=16.5402;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.0103;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.7273;NS=1;NUMALT=1;ODDS=10.4306;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=738;RO=11;RPL=1;RPP=3.0103;RPPR=4.78696;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:13:11,2:11:738:2:75:-0.695464,0,-29.8019
phiX174	3185	.	A	<*>	0	.	DP=7;END=3324;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	62297:7:0:63013:7:716:0
phiX174	3325	.	A	C	0.0705175	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=4.11232;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:284:2:58:-2.65031,0,-9.66348
phiX174	3326	.	G	<*>	0	.	DP=7;END=3412;MIN_DP=4	GQ:DP:MIN_DP:QR:RO:QA:AO	42447:7:4:42832:7:385:0
phiX174	3413	.	T	G	0.00284067	.	AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=7.33194;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:9,2:9:537:2:57:-1.59087,0,-22.4183
phiX174	3414	.	C	<*>	0	.	DP=10;END=3417;MIN_DP=10	GQ:DP:MIN_DP:QR:RO:QA:AO	2435:10:10:2491:9:56:0
phiX174	3418	.	A	C	0.000937887	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=8.44033;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:526:2:60:-1.49768,0,-21.0207
phiX174	3419	.	A	<*>	0	.	DP=7;END=3489;MIN_DP=3	GQ:DP:MIN_DP:QR:RO:QA:AO	32175:7:3:32478:7:303:0
phiX174	3490	.	A	C	0.00226584	.	AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=7.5581;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:9,2:9:543:2:66:-2.09471,0,-24.3433
phiX174	3491	.	T	<*>	0	.	DP=5;END=3728;MIN_DP=2	GQ:DP:MIN_DP:QR:RO:QA:AO	80198:5:2:80931:5:733:0
phiX174	3729	.	C	T	0.295112	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.65478;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:232:2:63:-3.28331,0,-11.7007
phiX174	3730	.	A	<*>	0	.	DP=6;END=4030;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	108927:6:0:110100:5:1173:0
phiX174	4031	.	T	G	0.0784807	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=4.00441;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:6,2:6:322:2:85:-3.02817,0,-11.6802
phiX174	4032	.	G	<*>	0	.	DP=6;END=4501;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	190881:6:0:192703:6:1822:0
phiX174	4502	.	A	C	0.232919	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.89868;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:284:2:55:-2.57533,0,-11.8832
phiX174	4503	.	T	<*>	0	.	DP=6;END=4557;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	20294:6:0:20521:6:227:0
phiX174	4558	.	C	G	0.076247	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=4.03372;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:204:2:59:-2.68445,0,-8.4362
phiX174	4559	.	T	<*>	0	.	DP=3;END=4654;MIN_DP=1	GQ:DP:MIN_DP:QR:RO:QA:AO	20927:3:1:21288:3:361:0
phiX174	4655	.	T	G	0.399408	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.33999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:193:2:70:-2.81796,0,-11.1489
phiX174	4656	.	G	<*>	0	.	DP=8;END=4703;MIN_DP=6	GQ:DP:MIN_DP:QR:RO:QA:AO	26170:8:6:26393:8:223:0
phiX174	4704	.	T	C	0.000171782	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.1378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:10,2:10:621:2:58:-1.1962,0,-26.2058
phiX174	4705	.	C	<*>	0	.	DP=7;END=5386;MIN_DP=0	GQ:DP:MIN_DP:QR:RO:QA:AO	291210:7:0:294344:6:3134:0