##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate==03/12/22
##ALT=<ID=SNP,Description="SNP">
##ALT=<ID=PH_SNPs,Description="Phased SNPs">
##ALT=<ID=INDEL,Description="Insertion-deletion">
##ALT=<ID=COMPLEX,Description="Complex variant, collection of SNPs and indels">
##INFO=<ID=VC,Number=1,Type=String,Description="Type (class) of variant">
##ALT=<ID=SIMPLE,Description="Graph bubble is simple">
##ALT=<ID=NESTED,Description="Variation site was a nested feature in the graph">
##ALT=<ID=TOO_MANY_ALTS,Description="Variation site was a multinested feature with too many alts to include all in the VCF">
##INFO=<ID=GRAPHTYPE,Number=1,Type=String,Description="Type of graph feature">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MEAN_FWD_COVG,Number=R,Type=Integer,Description="Mean forward coverage">
##FORMAT=<ID=MEAN_REV_COVG,Number=R,Type=Integer,Description="Mean reverse coverage">
##FORMAT=<ID=MED_FWD_COVG,Number=R,Type=Integer,Description="Med forward coverage">
##FORMAT=<ID=MED_REV_COVG,Number=R,Type=Integer,Description="Med reverse coverage">
##FORMAT=<ID=SUM_FWD_COVG,Number=R,Type=Integer,Description="Sum forward coverage">
##FORMAT=<ID=SUM_REV_COVG,Number=R,Type=Integer,Description="Sum reverse coverage">
##FORMAT=<ID=GAPS,Number=R,Type=Float,Description="Number of gap bases">
##FORMAT=<ID=LIKELIHOOD,Number=R,Type=Float,Description="Likelihood">
##FORMAT=<ID=GT_CONF,Number=1,Type=Float,Description="Genotype confidence">
##contig=<ID=gyrA>
##INFO=<ID=VARID,Number=.,Type=String,Description="The identifier for the panel variant(s) the record overlaps with">
##INFO=<ID=PREDICT,Number=.,Type=String,Description="The drug resistance prediction(s) for the corresponding VARID(s), where 'R' = resistant, 'S' = susceptible, 'F' = failed, and 'U' = unknown">
##INFO=<ID=OGT,Number=1,Type=String,Description="Original genotype after adjusting for minor allele depth proportions of 0.2">
##INFO=<ID=PDP,Number=R,Type=Float,Description="Proportion of the total position depth found on this allele">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
gyrA	67	f5435198	C	T	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=gyrA_C-34T;PREDICT=.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:61,0:46,0:61,0:46,0:61,0:46,0:0,1:-48.7159,-968.753:920.037
gyrA	161	1668b7fb	G	C	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=0,1;VARID=gyrA_E21Q;PREDICT=S	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:0,144:0,128:0,144:0,127:0,433:0,385:1,0:-1728.61,-6.04268:1722.56
gyrA	362	8eb75a0c	G	T	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=gyrA_G88N,gyrA_G88A,gyrA_G88C;PREDICT=.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:76,0:74,0:74,0:67,0:304,0:299,0:0.5,1:-141.18,-1166.78:1025.6
gyrA	369	a3f63686	CGT	CGC,TGT	.	PASS	VC=PH_SNPs;GRAPHTYPE=SIMPLE;PDP=0.740741,0.259259,0;VARID=gyrA_A90G,gyrA_A90V,gyrA_S91P;PREDICT=.,.,.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:101,37,0:99,33,0:148,0,0:134,0,0:304,148,0:298,134,0:0.333333,0.75,1:-408.473,-1184.91,-1719.4:776.441
gyrA	380	02a5e0a3	GACAG	AACAC,CACAC,GACAC,GCCAC,GGCAC,TACAC,TACAG	.	PASS	VC=PH_SNPs;GRAPHTYPE=NESTED;PDP=0,0,0,0.82392,0.17608,0,0,0;VARID=gyrA_D94Y,gyrA_D94G,gyrA_D94C,gyrA_D94H,gyrA_S95T,gyrA_D94N,gyrA_D94A;PREDICT=.,.,.,.,S,.,r	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	3:0,0,0,124,27,0,0,0:0,0,0,124,26,0,0,0:0,0,0,124,27,0,0,0:0,0,0,124,26,0,0,0:0,0,0,248,55,0,0,0:0,0,0,249,53,0,0,0:1,1,1,0,0,1,1,1:-1862.16,-1862.16,-1862.16,-247.957,-1250.38,-1862.16,-1862.16,-1862.16:1002.43
gyrA	839	f280b954	G	A	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=gyrA_G247S;PREDICT=.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:106,0:106,0:106,0:106,0:212,0:213,0:0,1:-5.07253,-1452.3:1447.22
gyrA	855	0cd176e8	G	T	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=gyrA_R252L;PREDICT=.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:104,0:106,0:103,0:102,0:314,0:320,0:0,1:-5.30863,-1443.09:1437.78
gyrA	1251	23d4ff8e	C	T	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=gyrA_A384V;PREDICT=.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:152,0:121,0:151,0:121,0:610,0:485,0:0,1:-6.17989,-1733.21:1727.03
gyrA	1487	e6760a86	G	T	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0;VARID=gyrA_A463S;PREDICT=.	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:101,0:136,0:100,0:134,0:405,0:547,0:0,1:-3.65542,-1567.43:1563.77
gyrA	2098	44abef99	GGCCGG	CGCCGA,GGCCGA	.	PASS	VC=PH_SNPs;GRAPHTYPE=SIMPLE;PDP=0.00403226,0,0.995968;VARID=gyrA_G668D;PREDICT=S	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	2:1,0,107:0,0,140:1,0,106:0,0,139:2,0,323:0,0,421:1,1,0:-1608,-1618.08,-8.4472:1599.56