##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate==11/01/23
##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=ahpC>
##contig=<ID=ddn>
##contig=<ID=eis>
##contig=<ID=embA>
##contig=<ID=embB>
##contig=<ID=ethA>
##contig=<ID=fabG1>
##contig=<ID=gid>
##contig=<ID=gyrA>
##contig=<ID=gyrB>
##contig=<ID=inhA>
##contig=<ID=katG>
##contig=<ID=pncA>
##contig=<ID=rplC>
##contig=<ID=rpoB>
##contig=<ID=rpsL>
##contig=<ID=rrs>
##contig=<ID=tlyA>
##FILTER=<ID=ld,Description="Kmer coverage on called allele less than 3">
##FILTER=<ID=sb,Description="A strand on the called allele has less than 1.00% of the coverage for that allele">
##FILTER=<ID=lgc,Description="Genotype confidence score less than 5.0">
##FILTER=<ID=frs,Description="Fraction of read support on called allele is less than 0">
##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 0.1">
##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
ethA	19	04dae167	T	C	.	ld;lgc	VC=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	.:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-144,-144:0
ethA	50	e701a0b8	AGTGTCGACATCTCGTTGACG	A	.	ld;lgc	VC=INDEL;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	.:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-144,-144:0
ethA	90	33aa4fa6	A	G	.	ld;lgc	VC=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	.:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-144,-144:0
ethA	191	902bd677	A	AGC	.	ld;lgc	VC=INDEL;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	.:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-144,-144:0
ethA	330	023f7fcf	A	G	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:18,0:23,0:17,0:23,0:54,0:71,0:0,1:-10.6909,-332.812:322.121
ethA	471	a8ef7b41	G	A	.	PASS	VC=SNP;GRAPHTYPE=SIMPLE;PDP=1,0	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:36,0:40,0:36,0:40,0:73,0:80,0:0,1:-3.19451,-493.993:490.798