test-annotated.vcf

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20191113
##source=freeBayes v1.3.1-dirty
##reference=reference/ref.fa
##contig=<ID=Chromosome,length=4411532>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-4411532"
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##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=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=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=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="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=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,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=Integer,Description="Sum of quality of the alternate observations">
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Wed Nov 13 23:01:34 2019
##bcftools_annotateVersion=1.9+htslib-1.9
##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Wed Nov 13 23:01:34 2019
##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -noStats -no-downstream -no-upstream -no-utr ref test.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	out
Chromosome	2532	.	C	T	404.531	.	AB=0;AO=14;DP=15;QA=471;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|dnaN|Rv0002|transcript|Rv0002|protein_coding|1/1|c.481C>T|p.Leu161Leu|481/1209|481/1209|161/402||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:14:471:-42.5477,-4.21442,0
Chromosome	9143	.	C	T	937.407	.	AB=0;AO=31;DP=31;QA=1071;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|gyrA|Rv0006|transcript|Rv0006|protein_coding|1/1|c.1842C>T|p.Ile614Ile|1842/2517|1842/2517|614/838||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1071:-96.6842,-9.33193,0
Chromosome	11370	.	C	T	907.162	.	AB=0;AO=29;DP=29;QA=1054;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|alaT-Rv0008c|Rvnt02-Rv0008c|intergenic_region|Rvnt02-Rv0008c|||n.11370C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1054:-95.1657,-8.72987,0
Chromosome	13460	.	G	A	769.671	.	AB=0;AO=25;DP=25;QA=897;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0010c|Rv0010c|transcript|Rv0010c|protein_coding|1/1|c.99C>T|p.Asp33Asp|99/426|99/426|33/141||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:897:-81.0378,-7.52575,0
Chromosome	14401	.	G	A	719.895	.	AB=0;AO=25;DP=26;QA=843;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0012|Rv0012|transcript|Rv0012|protein_coding|1/1|c.313G>A|p.Glu105Lys|313/789|313/789|105/262||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:25:843:-76.0204,-7.52575,0
Chromosome	15117	.	G	C	872.894	.	AB=0;AO=27;DP=27;QA=996;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|trpG|Rv0013|transcript|Rv0013|protein_coding|1/1|c.204G>C|p.Met68Ile|204/699|204/699|68/232||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:996:-89.953,-8.12781,0
Chromosome	22453	.	G	A	547.633	.	AB=0;AO=18;DP=18;QA=634;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|pstP|Rv0018c|transcript|Rv0018c|protein_coding|1/1|c.729C>T|p.Tyr243Tyr|729/1545|729/1545|243/514||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:634:-57.3724,-5.41854,0
Chromosome	23174	.	A	C	669.528	.	AB=0;AO=21;DP=21;QA=767;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|pstP|Rv0018c|transcript|Rv0018c|protein_coding|1/1|c.8T>G|p.Leu3Arg|8/1545|8/1545|3/514||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:767:-69.3546,-6.32163,0
Chromosome	27469	.	G	A	598.969	.	AB=0;AO=19;DP=19;QA=699;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|whiB5-Rv0023|Rv0022c-Rv0023|intergenic_region|Rv0022c-Rv0023|||n.27469G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:699:-63.2333,-5.71957,0
Chromosome	29482	.	CA	C	612.769	.	AB=0;AO=21;DP=22;QA=715;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv0025|Rv0025|transcript|Rv0025|protein_coding|1/1|c.241delA|p.Thr81fs|241/363|241/363|81/120||INFO_REALIGN_3_PRIME;LOF=(Rv0025|Rv0025|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:21:715:-64.2398,-6.32163,0
Chromosome	30519	.	C	T	644.771	.	AB=0;AO=21;DP=21;QA=770;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0026|Rv0026|transcript|Rv0026|protein_coding|1/1|c.798C>T|p.Gly266Gly|798/1347|798/1347|266/448||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:770:-69.6218,-6.32163,0
Chromosome	30688	.	T	G	708.366	.	AB=0;AO=22;DP=22;QA=814;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0026|Rv0026|transcript|Rv0026|protein_coding|1/1|c.967T>G|p.Ser323Ala|967/1347|967/1347|323/448||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:814:-73.5784,-6.62266,0
Chromosome	30943	.	C	T	568.148	.	AB=0;AO=20;DP=20;QA=654;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0026|Rv0026|transcript|Rv0026|protein_coding|1/1|c.1222C>T|p.Pro408Ser|1222/1347|1222/1347|408/448||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:654:-59.1596,-6.0206,0
Chromosome	31077	.	C	T	780.018	.	AB=0;AO=25;DP=25;QA=897;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0026-Rv0027|Rv0026-Rv0027|intergenic_region|Rv0026-Rv0027|||n.31077C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:897:-81.0384,-7.52575,0
Chromosome	32349	.	CCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATG	C	439.549	.	AB=0;AO=17;DP=17;QA=515;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv0029|Rv0029|transcript|Rv0029|protein_coding|1/1|c.295_331delCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATGC|p.Arg99fs|295/1098|295/1098|99/365||INFO_REALIGN_3_PRIME;LOF=(Rv0029|Rv0029|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:515:-46.6371,-5.11751,0
Chromosome	36538	.	C	T	887.15	.	AB=0;AO=28;DP=28;QA=1020;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|bioF2|Rv0032|transcript|Rv0032|protein_coding|1/1|c.2244C>T|p.Ser748Ser|2244/2316|2244/2316|748/771||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1020:-92.1057,-8.42884,0
Chromosome	39758	.	G	A	599.016	.	AB=0;AO=20;DP=20;QA=690;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0036c|Rv0036c|transcript|Rv0036c|protein_coding|1/1|c.72C>T|p.His24His|72/774|72/774|24/257||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:690:-62.4127,-6.0206,0
Chromosome	42281	.	A	C	686.46	.	AB=0;AO=22;DP=22;QA=794;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0039c|Rv0039c|transcript|Rv0039c|protein_coding|1/1|c.71T>G|p.Phe24Cys|71/348|71/348|24/115||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:794:-71.7748,-6.62266,0
Chromosome	43945	.	G	A	954.753	.	AB=0;AO=30;DP=30;QA=1087;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|leuS|Rv0041|transcript|Rv0041|protein_coding|1/1|c.384G>A|p.Val128Val|384/2910|384/2910|128/969||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1087:-98.1364,-9.0309,0
Chromosome	51750	.	C	T	866.513	.	AB=0;AO=28;DP=28;QA=1006;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0047c-Rv0048c|Rv0047c-Rv0048c|intergenic_region|Rv0047c-Rv0048c|||n.51750C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1006:-90.8441,-8.42884,0
Chromosome	51954	.	T	A	827.037	.	AB=0;AO=26;DP=26;QA=953;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0048c|Rv0048c|transcript|Rv0048c|protein_coding|1/1|c.744A>T|p.Glu248Asp|744/870|744/870|248/289||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:953:-86.0852,-7.82678,0
Chromosome	53785	.	C	G	873.695	.	AB=0;AO=28;DP=28;QA=1015;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ponA1|Rv0050|transcript|Rv0050|protein_coding|1/1|c.123C>G|p.Ile41Met|123/2037|123/2037|41/678||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1015:-91.6475,-8.42884,0
Chromosome	57393	.	A	T	493.548	.	AB=0;AO=16;DP=16;QA=581;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0051-Rv0052|Rv0051-Rv0052|intergenic_region|Rv0051-Rv0052|||n.57393A>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:581:-52.6202,-4.81648,0
Chromosome	62657	.	G	A	803.258	.	AB=0;AO=25;DP=25;QA=919;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|dnaB|Rv0058|transcript|Rv0058|protein_coding|1/1|c.2262G>A|p.Pro754Pro|2262/2625|2262/2625|754/874||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:919:-83.0236,-7.52575,0
Chromosome	66249	.	T	G	688.983	.	AB=0;AO=22;DP=22;QA=795;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|celA1|Rv0062|transcript|Rv0062|protein_coding|1/1|c.698T>G|p.Leu233Arg|698/1143|698/1143|233/380||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:795:-71.868,-6.62266,0
Chromosome	66285	.	C	G	724.391	.	AB=0;AO=23;DP=23;QA=831;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|celA1|Rv0062|transcript|Rv0062|protein_coding|1/1|c.734C>G|p.Ala245Gly|734/1143|734/1143|245/380||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:831:-75.1083,-6.92369,0
Chromosome	69871	.	C	T	676.463	.	AB=0;AO=23;DP=23;QA=782;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0064|Rv0064|transcript|Rv0064|protein_coding|1/1|c.1252C>T|p.Leu418Phe|1252/2940|1252/2940|418/979||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:782:-70.6836,-6.92369,0
Chromosome	70267	.	T	G	810.419	.	AB=0;AO=26;DP=26;QA=936;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0064|Rv0064|transcript|Rv0064|protein_coding|1/1|c.1648T>G|p.Phe550Val|1648/2940|1648/2940|550/979||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:936:-84.5525,-7.82678,0
Chromosome	74390	.	G	A	763.669	.	AB=0;AO=26;DP=26;QA=874;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|icd2|Rv0066c|transcript|Rv0066c|protein_coding|1/1|c.122C>T|p.Ala41Val|122/2238|122/2238|41/745||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:874:-78.9574,-7.82678,0
Chromosome	75264	.	C	T	740.688	.	AB=0;AO=24;DP=24;QA=849;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0067c-Rv0068|Rv0067c-Rv0068|intergenic_region|Rv0067c-Rv0068|||n.75264C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:849:-76.7259,-7.22472,0
Chromosome	83982	.	A	G	711.249	.	AB=0;AO=22;DP=22;QA=818;QR=0;RO=0;TYPE=snp;ANN=G|splice_region_variant&stop_retained_variant|LOW|Rv0074|Rv0074|transcript|Rv0074|protein_coding|1/1|c.1235A>G|p.Ter412Ter|1235/1236|1235/1236|412/411||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:818:-73.9429,-6.62266,0
Chromosome	89200	.	T	G	868.533	.	AB=0;AO=28;DP=28;QA=998;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0080|Rv0080|transcript|Rv0080|protein_coding|1/1|c.179T>G|p.Val60Gly|179/459|179/459|60/152||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:998:-90.1239,-8.42884,0
Chromosome	95591	.	G	T	1055.19	.	AB=0;AO=33;DP=33;QA=1202;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained|HIGH|hycE|Rv0087|transcript|Rv0087|protein_coding|1/1|c.178G>T|p.Glu60*|178/1479|178/1479|60/492||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1202:-108.479,-9.93399,0
Chromosome	97388	.	G	T	738.317	.	AB=0;AO=24;DP=24;QA=845;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0088|Rv0088|transcript|Rv0088|protein_coding|1/1|c.462G>T|p.Trp154Cys|462/675|462/675|154/224||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:845:-76.3493,-7.22472,0
Chromosome	97696	.	C	T	590.886	.	AB=0;AO=20;DP=20;QA=683;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0088-Rv0089|Rv0088-Rv0089|intergenic_region|Rv0088-Rv0089|||n.97696C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:683:-61.7692,-6.0206,0
Chromosome	103600	.	G	A	913.672	.	AB=0;AO=28;DP=28;QA=1048;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0093c|Rv0093c|transcript|Rv0093c|protein_coding|1/1|c.64C>T|p.Arg22Cys|64/849|64/849|22/282||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1048:-94.6304,-8.42884,0
Chromosome	104824	.	A	C	766.276	.	AB=0;AO=25;DP=25;QA=887;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0095c|Rv0095c|transcript|Rv0095c|protein_coding|1/1|c.392T>G|p.Ile131Ser|392/411|392/411|131/136||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:887:-80.142,-7.52575,0
Chromosome	104941	.	CCGA	TGGG	626.976	.	AB=0;AO=21;DP=21;QA=728;QR=0;RO=0;TYPE=complex;ANN=TGGG|missense_variant|MODERATE|Rv0095c|Rv0095c|transcript|Rv0095c|protein_coding|1/1|c.272_275delTCGGinsCCCA|p.ValGly91AlaGln|275/411|272/411|91/136||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:728:-65.8331,-6.32163,0
Chromosome	104962	.	G	A	658.257	.	AB=0;AO=21;DP=21;QA=768;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0095c|Rv0095c|transcript|Rv0095c|protein_coding|1/1|c.254C>T|p.Ala85Val|254/411|254/411|85/136||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:768:-69.4431,-6.32163,0
Chromosome	105060	.	GTCG	ATCA	500.119	.	AB=0;AO=16;DP=16;QA=585;QR=0;RO=0;TYPE=complex;ANN=ATCA|synonymous_variant|LOW|Rv0095c|Rv0095c|transcript|Rv0095c|protein_coding|1/1|c.153_156delCGACinsTGAT|p.53|156/411|153/411|51/136||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:585:-52.653,-4.81648,0
Chromosome	112247	.	A	G	375.829	.	AB=0;AO=12;DP=12;QA=446;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|nrp|Rv0101|transcript|Rv0101|protein_coding|1/1|c.2247A>G|p.Ala749Ala|2247/7539|2247/7539|749/2512||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:446:-40.4842,-3.61236,0
Chromosome	123520	.	C	T	1081.64	.	AB=0;AO=34;DP=34;QA=1230;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0104|Rv0104|transcript|Rv0104|protein_coding|1/1|c.1204C>T|p.His402Tyr|1204/1515|1204/1515|402/504||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1230:-110.989,-10.235,0
Chromosome	125830	.	G	GA	756.492	.	AB=0;AO=25;DP=26;QA=869;QR=0;RO=0;TYPE=ins;ANN=GA|frameshift_variant|HIGH|ctpI|Rv0107c|transcript|Rv0107c|protein_coding|1/1|c.4711dupT|p.Ser1571fs|4711/4899|4711/4899|1571/1632||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:25:869:-78.1453,-7.52575,0
Chromosome	126803	.	G	A	676.991	.	AB=0;AO=22;DP=22;QA=780;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ctpI|Rv0107c|transcript|Rv0107c|protein_coding|1/1|c.3739C>T|p.Pro1247Ser|3739/4899|3739/4899|1247/1632||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:780:-70.517,-6.62266,0
Chromosome	131174	.	T	TG	534.072	.	AB=0;AO=19;DP=19;QA=624;QR=0;RO=0;TYPE=ins;ANN=TG|intergenic_region|MODIFIER|Rv0108c-PE_PGRS1|Rv0108c-Rv0109|intergenic_region|Rv0108c-Rv0109|||n.131174_131175insG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:624:-56.4645,-5.71957,0
Chromosome	137850	.	GT	G	442.684	.	AB=0;AO=15;DP=15;QA=518;QR=0;RO=0;TYPE=del;ANN=G|frameshift_variant|HIGH|gmhA|Rv0113|transcript|Rv0113|protein_coding|1/1|c.537delT|p.Phe179fs|537/591|537/591|179/196||INFO_REALIGN_3_PRIME;LOF=(gmhA|Rv0113|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:518:-46.9384,-4.51545,0
Chromosome	139756	.	C	T	654.233	.	AB=0;AO=22;DP=22;QA=760;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|hddA-Rv0115a|Rv0115-Rv0115a|intergenic_region|Rv0115-Rv0115a|||n.139756C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:760:-68.7062,-6.62266,0
Chromosome	143207	.	C	T	798.544	.	AB=0;AO=26;DP=26;QA=912;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|oxcA|Rv0118c|transcript|Rv0118c|protein_coding|1/1|c.670G>A|p.Gly224Ser|670/1749|670/1749|224/582||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:912:-82.3801,-7.82678,0
Chromosome	144390	.	G	A	476.739	.	AB=0;AO=15;DP=15;QA=557;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|fadD7|Rv0119|transcript|Rv0119|protein_coding|1/1|c.342G>A|p.Ala114Ala|342/1578|342/1578|114/525||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:557:-50.468,-4.51545,0
Chromosome	147985	.	C	T	863.429	.	AB=0;AO=28;DP=28;QA=995;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0121c|Rv0121c|transcript|Rv0121c|protein_coding|1/1|c.358G>A|p.Ala120Thr|358/435|358/435|120/144||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:995:-89.8475,-8.42884,0
Chromosome	155293	.	G	A	529.823	.	AB=0;AO=17;DP=17;QA=616;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|mak|Rv0127|transcript|Rv0127|protein_coding|1/1|c.1062G>A|p.Pro354Pro|1062/1368|1062/1368|354/455||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:616:-55.7639,-5.11751,0
Chromosome	163573	.	A	C	779.911	.	AB=0;AO=24;DP=24;QA=891;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|cyp138|Rv0136|transcript|Rv0136|protein_coding|1/1|c.208A>C|p.Arg70Arg|208/1326|208/1326|70/441||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:891:-80.5087,-7.22472,0
Chromosome	174684	.	C	A	483.623	.	AB=0;AO=16;DP=16;QA=569;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0147|Rv0147|transcript|Rv0147|protein_coding|1/1|c.1447C>A|p.Arg483Arg|1447/1521|1447/1521|483/506||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:569:-51.5386,-4.81648,0
Chromosome	177596	.	T	C	682.146	.	AB=0;AO=21;DP=21;QA=781;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|PE1|Rv0151c|transcript|Rv0151c|protein_coding|1/1|c.1714A>G|p.Ile572Val|1714/1767|1714/1767|572/588||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:781:-70.6164,-6.32163,0
Chromosome	178946	.	C	T	661.486	.	AB=0;AO=22;DP=22;QA=769;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PE1|Rv0151c|transcript|Rv0151c|protein_coding|1/1|c.364G>A|p.Ala122Thr|364/1767|364/1767|122/588||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:769:-69.5225,-6.62266,0
Chromosome	187738	.	G	A	1032.45	.	AB=0;AO=34;DP=34;QA=1176;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|PE3|Rv0159c|transcript|Rv0159c|protein_coding|1/1|c.1102C>T|p.Arg368Trp|1102/1407|1102/1407|368/468||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1176:-106.12,-10.235,0
Chromosome	195360	.	C	T	657.334	.	AB=0;AO=21;DP=21;QA=758;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|fadD5|Rv0166|transcript|Rv0166|protein_coding|1/1|c.368C>T|p.Ala123Val|368/1665|368/1665|123/554||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:758:-68.5379,-6.32163,0
Chromosome	199470	.	G	T	1042.92	.	AB=0;AO=34;DP=34;QA=1192;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|mce1A|Rv0169|transcript|Rv0169|protein_coding|1/1|c.937G>T|p.Ala313Ser|937/1365|937/1365|313/454||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1192:-107.571,-10.235,0
Chromosome	200332	.	C	A	805.364	.	AB=0;AO=27;DP=27;QA=924;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|mce1B|Rv0170|transcript|Rv0170|protein_coding|1/1|c.438C>A|p.Phe146Leu|438/1041|438/1041|146/346||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:924:-83.4492,-8.12781,0
Chromosome	208316	.	A	AT	488.826	.	AB=0;AO=18;DP=19;QA=577;QR=0;RO=0;TYPE=ins;ANN=AT|frameshift_variant|HIGH|Rv0176|Rv0176|transcript|Rv0176|protein_coding|1/1|c.866dupT|p.Ser290fs|867/969|867/969|289/322||INFO_REALIGN_3_PRIME;LOF=(Rv0176|Rv0176|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:18:577:-51.864,-5.41854,0
Chromosome	208321	.	CG	T	549.319	.	AB=0;AO=17;DP=18;QA=640;QR=0;RO=0;TYPE=complex;ANN=T|frameshift_variant&synonymous_variant|HIGH|Rv0176|Rv0176|transcript|Rv0176|protein_coding|1/1|c.870_871delCGinsT|p.Ala291fs|870/969|870/969|290/322||;LOF=(Rv0176|Rv0176|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:17:640:-57.5172,-5.11751,0
Chromosome	216586	.	A	G	747.01	.	AB=0;AO=24;DP=24;QA=860;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|bglS|Rv0186|transcript|Rv0186|protein_coding|1/1|c.318A>G|p.Gln106Gln|318/2076|318/2076|106/691||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:860:-77.7102,-7.22472,0
Chromosome	217201	.	C	T	713.331	.	AB=0;AO=23;DP=23;QA=818;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|bglS|Rv0186|transcript|Rv0186|protein_coding|1/1|c.933C>T|p.Asn311Asn|933/2076|933/2076|311/691||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:818:-73.9299,-6.92369,0
Chromosome	220050	.	C	T	779.885	.	AB=0;AO=26;DP=27;QA=945;QR=33;RO=1;TYPE=snp;ANN=T|synonymous_variant|LOW|ilvD|Rv0189c|transcript|Rv0189c|protein_coding|1/1|c.1674G>A|p.Leu558Leu|1674/1728|1674/1728|558/575||	GT:DP:RO:QR:AO:QA:GL	1/1:27:1:33:26:945:-82.0591,-4.82868,0
Chromosome	223752	.	G	C	259.981	.	AB=0;AO=10;DP=11;QA=344;QR=33;RO=1;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv0192|Rv0192|transcript|Rv0192|protein_coding|1/1|c.189G>C|p.Gly63Gly|189/1101|189/1101|63/366||	GT:DP:RO:QR:AO:QA:GL	1/1:11:1:33:10:344:-27.9922,-0.0121952,0
Chromosome	225668	.	T	C	722.014	.	AB=0;AO=23;DP=23;QA=826;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0193c|Rv0193c|transcript|Rv0193c|protein_coding|1/1|c.904A>G|p.Ser302Gly|904/1848|904/1848|302/615||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:826:-74.652,-6.92369,0
Chromosome	232574	.	G	T	479.244	.	AB=0;AO=17;DP=17;QA=560;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0197|Rv0197|transcript|Rv0197|protein_coding|1/1|c.344G>T|p.Gly115Val|344/2289|344/2289|115/762||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:560:-50.706,-5.11751,0
Chromosome	233358	.	C	A	650.381	.	AB=0;AO=21;DP=21;QA=745;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0197|Rv0197|transcript|Rv0197|protein_coding|1/1|c.1128C>A|p.Val376Val|1128/2289|1128/2289|376/762||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:745:-67.3607,-6.32163,0
Chromosome	233364	.	C	G	535.374	.	AB=0;AO=18;DP=19;QA=628;QR=14;RO=1;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0197|Rv0197|transcript|Rv0197|protein_coding|1/1|c.1134C>G|p.Ser378Arg|1134/2289|1134/2289|378/762||	GT:DP:RO:QR:AO:QA:GL	1/1:19:1:14:18:628:-55.4317,-4.31958,0
Chromosome	234494	.	T	TGC	490.417	.	AB=0;AO=16;DP=16;QA=580;QR=0;RO=0;TYPE=ins;ANN=TGC|frameshift_variant|HIGH|Rv0197|Rv0197|transcript|Rv0197|protein_coding|1/1|c.2265_2266insCG|p.Ser756fs|2266/2289|2266/2289|756/762||INFO_REALIGN_3_PRIME	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:580:-52.5324,-4.81648,0
Chromosome	243598	.	G	A	468.615	.	AB=0;AO=16;DP=16;QA=543;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0205|Rv0205|transcript|Rv0205|protein_coding|1/1|c.215G>A|p.Arg72His|215/1104|215/1104|72/367||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:543:-49.1882,-4.81648,0
Chromosome	249522	.	C	T	684.059	.	AB=0;AO=23;DP=23;QA=797;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0209|Rv0209|transcript|Rv0209|protein_coding|1/1|c.485C>T|p.Ala162Val|485/1086|485/1086|162/361||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:797:-72.0386,-6.92369,0
Chromosome	251468	.	G	T	737.505	.	AB=0;AO=24;DP=24;QA=860;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0210|Rv0210|transcript|Rv0210|protein_coding|1/1|c.1349G>T|p.Arg450Leu|1349/1479|1349/1479|450/492||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:860:-77.7106,-7.22472,0
Chromosome	251575	.	A	G	571.66	.	AB=0;AO=19;DP=19;QA=689;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0210|Rv0210|transcript|Rv0210|protein_coding|1/1|c.1456A>G|p.Thr486Ala|1456/1479|1456/1479|486/492||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:689:-62.3348,-5.71957,0
Chromosome	251669	.	C	T	697.305	.	AB=0;AO=23;DP=23;QA=806;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0210-pckA|Rv0210-Rv0211|intergenic_region|Rv0210-Rv0211|||n.251669C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:806:-72.8403,-6.92369,0
Chromosome	260282	.	T	G	455.367	.	AB=0;AO=15;DP=15;QA=537;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|lipW|Rv0217c|transcript|Rv0217c|protein_coding|1/1|c.550A>C|p.Thr184Pro|550/909|550/909|184/302||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:537:-48.6618,-4.51545,0
Chromosome	265968	.	C	G	547.647	.	AB=0;AO=18;DP=18;QA=635;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|echA1|Rv0222|transcript|Rv0222|protein_coding|1/1|c.462C>G|p.Arg154Arg|462/789|462/789|154/262||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:635:-57.4695,-5.41854,0
Chromosome	284623	.	G	A	593.461	.	AB=0;AO=20;DP=20;QA=707;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|aftD|Rv0236c|transcript|Rv0236c|protein_coding|1/1|c.2229C>T|p.Thr743Thr|2229/4203|2229/4203|743/1400||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:707:-63.9437,-6.0206,0
Chromosome	293628	.	A	AC	372.967	.	AB=0;AO=13;DP=14;QA=467;QR=35;RO=1;TYPE=ins;ANN=AC|intragenic_variant|MODIFIER|F6|RVnc0008|gene_variant|RVnc0008|||n.293628_293629insC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:1:35:13:467:-38.8104,-0.715791,0
Chromosome	302200	.	C	T	350.586	.	AB=0;AO=12;DP=12;QA=409;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|hsp|Rv0251c|transcript|Rv0251c|protein_coding|1/1|c.453G>A|p.Gln151Gln|453/480|453/480|151/159||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:409:-37.1325,-3.61236,0
Chromosome	304679	.	G	T	814.977	.	AB=0;AO=25;DP=25;QA=932;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|nirB|Rv0252|transcript|Rv0252|protein_coding|1/1|c.1814G>T|p.Gly605Val|1814/2562|1814/2562|605/853||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:932:-84.1954,-7.52575,0
Chromosome	309765	.	T	C	1385.89	.	AB=0;AO=43;DP=43;QA=1584;QR=0;RO=0;TYPE=snp;ANN=C|stop_lost|HIGH|Rv0257|Rv0257|transcript|Rv0257|protein_coding|1/1|c.67T>C|p.Ter23Argext*?|67/375|67/375|23/124||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:43:1584:-142.833,-12.9443,0
Chromosome	320038	.	G	A	444.961	.	AB=0;AO=15;DP=16;QA=521;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|oplA|Rv0266c|transcript|Rv0266c|protein_coding|1/1|c.1117C>T|p.Pro373Ser|1117/3630|1117/3630|373/1209||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:15:521:-47.0569,-4.51545,0
Chromosome	320180	.	G	A	524.266	.	AB=0;AO=18;DP=18;QA=604;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|oplA|Rv0266c|transcript|Rv0266c|protein_coding|1/1|c.975C>T|p.Ile325Ile|975/3630|975/3630|325/1209||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:604:-54.6675,-5.41854,0
Chromosome	325505	.	C	T	1186.91	.	AB=0;AO=38;DP=38;QA=1356;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|fadD2|Rv0270|transcript|Rv0270|protein_coding|1/1|c.939C>T|p.Val313Val|939/1683|939/1683|313/560||	GT:DP:RO:QR:AO:QA:GL	1/1:38:0:0:38:1356:-122.329,-11.4391,0
Chromosome	328641	.	G	T	1118.23	.	AB=0;AO=38;DP=38;QA=1288;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0272c|Rv0272c|transcript|Rv0272c|protein_coding|1/1|c.1068C>A|p.Thr356Thr|1068/1134|1068/1134|356/377||	GT:DP:RO:QR:AO:QA:GL	1/1:38:0:0:38:1288:-116.196,-11.4391,0
Chromosome	331588	.	A	G	578.478	.	AB=0;AO=18;DP=18;QA=665;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0275c|Rv0275c|transcript|Rv0275c|protein_coding|1/1|c.71T>C|p.Leu24Ser|71/726|71/726|24/241||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:665:-60.1802,-5.41854,0
Chromosome	333212	.	C	G	615.939	.	AB=0;AO=20;DP=20;QA=731;QR=0;RO=0;TYPE=snp;ANN=G|intragenic_variant|MODIFIER|vapB25|Rv0277A|gene_variant|Rv0277A|||n.333212C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:731:-66.1155,-6.0206,0
Chromosome	333292	.	G	A	524.793	.	AB=0;AO=20;DP=20;QA=623;QR=0;RO=0;TYPE=snp;ANN=A|intragenic_variant|MODIFIER|vapB25|Rv0277A|gene_variant|Rv0277A|||n.333292G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:623:-56.361,-6.0206,0
Chromosome	336191	.	C	T	292.598	.	AB=0;AO=10;DP=10;QA=369;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0278c|Rv0278c|transcript|Rv0278c|protein_coding|1/1|c.120G>A|p.Met40Ile|120/2874|120/2874|40/957||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:369:-33.5583,-3.0103,0
Chromosome	338844	.	AC	GT	326.969	.	AB=0;AO=11;DP=11;QA=393;QR=0;RO=0;TYPE=complex;ANN=GT|missense_variant|MODERATE|PE_PGRS4|Rv0279c|transcript|Rv0279c|protein_coding|1/1|c.229_230delGTinsAC|p.Val77Thr|230/2514|229/2514|77/837||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:393:-35.7074,-3.31133,0
Chromosome	340953	.	G	T	659.549	.	AB=0;AO=21;DP=21;QA=756;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|PPE3|Rv0280|transcript|Rv0280|protein_coding|1/1|c.1590G>T|p.Ala530Ala|1590/1611|1590/1611|530/536||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:756:-68.3567,-6.32163,0
Chromosome	342146	.	C	A	972.674	.	AB=0;AO=32;DP=32;QA=1116;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|eccA3|Rv0282|transcript|Rv0282|protein_coding|1/1|c.17C>A|p.Ala6Glu|17/1896|17/1896|6/631||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1116:-100.731,-9.63296,0
Chromosome	343281	.	C	G	790.018	.	AB=0;AO=27;DP=27;QA=907;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|eccA3|Rv0282|transcript|Rv0282|protein_coding|1/1|c.1152C>G|p.Ala384Ala|1152/1896|1152/1896|384/631||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:907:-81.9166,-8.12781,0
Chromosome	350489	.	C	G	498.646	.	AB=0;AO=16;DP=16;QA=574;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|PPE4|Rv0286|transcript|Rv0286|protein_coding|1/1|c.555C>G|p.Ala185Ala|555/1542|555/1542|185/513||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:574:-51.9853,-4.81648,0
Chromosome	361415	.	G	A	684.844	.	AB=0;AO=22;DP=22;QA=787;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|PE_PGRS5|Rv0297|transcript|Rv0297|protein_coding|1/1|c.82G>A|p.Ala28Thr|82/1776|82/1776|28/591||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:787:-71.1483,-6.62266,0
Chromosome	367471	.	A	G	372.664	.	AB=0;AO=13;DP=13;QA=436;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|PPE5|Rv0304c|transcript|Rv0304c|protein_coding|1/1|c.5294T>C|p.Phe1765Ser|5294/6615|5294/6615|1765/2204||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:436:-39.5529,-3.91339,0
Chromosome	373282	.	TA	T	796.137	.	AB=0;AO=26;DP=26;QA=910;QR=0;RO=0;TYPE=del;ANN=T|frameshift_variant|HIGH|PPE6|Rv0305c|transcript|Rv0305c|protein_coding|1/1|c.2429delT|p.Leu810fs|2429/2892|2429/2892|810/963||;LOF=(PPE6|Rv0305c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:910:-82.2042,-7.82678,0
Chromosome	381030	.	G	A	890.014	.	AB=0;AO=28;DP=28;QA=1015;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0312|Rv0312|transcript|Rv0312|protein_coding|1/1|c.475G>A|p.Gly159Ser|475/1863|475/1863|159/620||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1015:-91.658,-8.42884,0
Chromosome	382984	.	G	A	1137.11	.	AB=0;AO=36;DP=36;QA=1304;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0314c|Rv0314c|transcript|Rv0314c|protein_coding|1/1|c.558C>T|p.Ser186Ser|558/663|558/663|186/220||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1304:-117.645,-10.8371,0
Chromosome	388725	.	C	T	603.531	.	AB=0;AO=20;DP=20;QA=695;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|dcd|Rv0321|transcript|Rv0321|protein_coding|1/1|c.144C>T|p.Tyr48Tyr|144/573|144/573|48/190||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:695:-62.8643,-6.0206,0
Chromosome	392261	.	C	T	650.637	.	AB=0;AO=21;DP=21;QA=756;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained&splice_region_variant|HIGH|Rv0325|Rv0325|transcript|Rv0325|protein_coding|1/1|c.223C>T|p.Gln75*|223/225|223/225|75/74||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:756:-68.3576,-6.32163,0
Chromosome	395784	.	G	A	589.776	.	AB=0;AO=21;DP=21;QA=684;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0330c|Rv0330c|transcript|Rv0330c|protein_coding|1/1|c.304C>T|p.Leu102Phe|304/741|304/741|102/246||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:684:-61.8613,-6.32163,0
Chromosome	397275	.	G	C	354.077	.	AB=0;AO=12;DP=12;QA=422;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0331|Rv0331|transcript|Rv0331|protein_coding|1/1|c.1075G>C|p.Ala359Pro|1075/1167|1075/1167|359/388||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:422:-38.309,-3.61236,0
Chromosome	405750	.	T	G	583.757	.	AB=0;AO=18;DP=18;QA=676;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0338c|Rv0338c|transcript|Rv0338c|protein_coding|1/1|c.92A>C|p.Tyr31Ser|92/2649|92/2649|31/882||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:676:-61.1731,-5.41854,0
Chromosome	412280	.	G	T	783.661	.	AB=0;AO=24;DP=24;QA=903;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|iniA|Rv0342|transcript|Rv0342|protein_coding|1/1|c.1443G>T|p.Gln481His|1443/1923|1443/1923|481/640||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:903:-81.5886,-7.22472,0
Chromosome	424320	.	T	TC	554.982	.	AB=0;AO=19;DP=20;QA=643;QR=0;RO=0;TYPE=ins;ANN=TC|frameshift_variant|HIGH|PPE7|Rv0354c|transcript|Rv0354c|protein_coding|1/1|c.374dupG|p.Ile126fs|374/426|374/426|125/141||;LOF=(PPE7|Rv0354c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:19:643:-57.8473,-5.71957,0
Chromosome	424932	.	A	T	437.254	.	AB=0;AO=15;DP=15;QA=517;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE8|Rv0355c|transcript|Rv0355c|protein_coding|1/1|c.9748T>A|p.Phe3250Ile|9748/9903|9748/9903|3250/3300||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:517:-46.8506,-4.51545,0
Chromosome	428698	.	T	C	706.756	.	AB=0;AO=23;DP=23;QA=824;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|PPE8|Rv0355c|transcript|Rv0355c|protein_coding|1/1|c.5982A>G|p.Ala1994Ala|5982/9903|5982/9903|1994/3300||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:824:-74.4718,-6.92369,0
Chromosome	429171	.	C	T	392.969	.	AB=0;AO=13;DP=13;QA=464;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE8|Rv0355c|transcript|Rv0355c|protein_coding|1/1|c.5509G>A|p.Ala1837Thr|5509/9903|5509/9903|1837/3300||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:464:-42.0939,-3.91339,0
Chromosome	433539	.	T	C	553.793	.	AB=0;AO=18;DP=18;QA=647;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|PPE8|Rv0355c|transcript|Rv0355c|protein_coding|1/1|c.1141A>G|p.Met381Val|1141/9903|1141/9903|381/3300||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:647:-58.5582,-5.41854,0
Chromosome	438271	.	A	G	604.459	.	AB=0;AO=19;DP=19;QA=697;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0359|Rv0359|transcript|Rv0359|protein_coding|1/1|c.754A>G|p.Thr252Ala|754/780|754/780|252/259||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:697:-63.0583,-5.71957,0
Chromosome	445780	.	T	C	678.927	.	AB=0;AO=22;DP=22;QA=796;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0368c|Rv0368c|transcript|Rv0368c|protein_coding|1/1|c.746A>G|p.His249Arg|746/1212|746/1212|249/403||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:796:-71.9593,-6.62266,0
Chromosome	447442	.	T	C	997.271	.	AB=0;AO=33;DP=33;QA=1136;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0370c|Rv0370c|transcript|Rv0370c|protein_coding|1/1|c.602A>G|p.Glu201Gly|602/897|602/897|201/298||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1136:-102.533,-9.93399,0
Chromosome	455325	.	GGGGC	CGGGT	698.954	.	AB=0;AO=23;DP=23;QA=807;QR=0;RO=0;TYPE=complex;ANN=CGGGT|missense_variant|MODERATE|Rv0377|Rv0377|transcript|Rv0377|protein_coding|1/1|c.905_909delGGGGCinsCGGGT|p.Arg302Pro|905/966|905/966|302/321||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:807:-72.6373,-6.92369,0
Chromosome	463974	.	T	C	580.217	.	AB=0;AO=19;DP=19;QA=678;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv0386|Rv0386|transcript|Rv0386|protein_coding|1/1|c.564T>C|p.His188His|564/3258|564/3258|188/1085||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:678:-61.3423,-5.71957,0
Chromosome	467504	.	GACGC	AACGGCG	316.921	.	AB=0;AO=11;DP=11;QA=388;QR=0;RO=0;TYPE=complex;ANN=AACGGCG|intragenic_variant|MODIFIER|Rv0387c|Rv0387c|gene_variant|Rv0387c|||n.467504_467508delGACGCinsAACGGCG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:388:-35.2554,-3.31133,0
Chromosome	467516	.	G	C	371.378	.	AB=0;AO=13;DP=13;QA=448;QR=0;RO=0;TYPE=snp;ANN=C|intragenic_variant|MODIFIER|Rv0387c|Rv0387c|gene_variant|Rv0387c|||n.467516G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:448:-40.6417,-3.91339,0
Chromosome	467526	.	C	G	436.403	.	AB=0;AO=14;DP=14;QA=511;QR=0;RO=0;TYPE=snp;ANN=G|intragenic_variant|MODIFIER|Rv0387c|Rv0387c|gene_variant|Rv0387c|||n.467526C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:511:-46.328,-4.21442,0
Chromosome	468357	.	G	A	721.159	.	AB=0;AO=23;DP=23;QA=830;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|purT|Rv0389|transcript|Rv0389|protein_coding|1/1|c.23G>A|p.Gly8Glu|23/1260|23/1260|8/419||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:830:-75.007,-6.92369,0
Chromosome	489073	.	C	G	728.914	.	AB=0;AO=23;DP=23;QA=836;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|pks6|Rv0405|transcript|Rv0405|protein_coding|1/1|c.3343C>G|p.Leu1115Val|3343/4209|3343/4209|1115/1402||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:836:-75.5607,-6.92369,0
Chromosome	491742	.	C	T	504.076	.	AB=0;AO=16;DP=16;QA=588;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|fgd1|Rv0407|transcript|Rv0407|protein_coding|1/1|c.960C>T|p.Phe320Phe|960/1011|960/1011|320/336||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:588:-53.2548,-4.81648,0
Chromosome	492150	.	C	G	375.085	.	AB=0;AO=12;DP=12;QA=439;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|pta|Rv0408|transcript|Rv0408|protein_coding|1/1|c.365C>G|p.Ala122Gly|365/2073|365/2073|122/690||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:439:-39.8535,-3.61236,0
Chromosome	498531	.	G	A	821.486	.	AB=0;AO=26;DP=26;QA=941;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0412c|Rv0412c|transcript|Rv0412c|protein_coding|1/1|c.1089C>T|p.Ala363Ala|1089/1320|1089/1320|363/439||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:941:-84.9987,-7.82678,0
Chromosome	501615	.	C	G	964.148	.	AB=0;AO=30;DP=30;QA=1105;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|thiO|Rv0415|transcript|Rv0415|protein_coding|1/1|c.468C>G|p.Leu156Leu|468/1023|468/1023|156/340||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1105:-99.7548,-9.0309,0
Chromosome	505974	.	A	G	538.742	.	AB=0;AO=18;DP=18;QA=622;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|lpqM|Rv0419|transcript|Rv0419|protein_coding|1/1|c.889A>G|p.Thr297Ala|889/1497|889/1497|297/498||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:622:-56.2992,-5.41854,0
Chromosome	514245	.	C	T	969.981	.	AB=0;AO=34;DP=34;QA=1105;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ctpH|Rv0425c|transcript|Rv0425c|protein_coding|1/1|c.1077G>A|p.Val359Val|1077/4620|1077/4620|359/1539||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1105:-99.7234,-10.235,0
Chromosome	514657	.	G	T	825.946	.	AB=0;AO=27;DP=27;QA=946;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ctpH|Rv0425c|transcript|Rv0425c|protein_coding|1/1|c.665C>A|p.Ala222Glu|665/4620|665/4620|222/1539||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:946:-85.4454,-8.12781,0
Chromosome	514684	.	C	T	777.753	.	AB=0;AO=25;DP=25;QA=902;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ctpH|Rv0425c|transcript|Rv0425c|protein_coding|1/1|c.638G>A|p.Arg213His|638/4620|638/4620|213/1539||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:902:-81.4938,-7.52575,0
Chromosome	517358	.	C	T	858.387	.	AB=0;AO=28;DP=28;QA=982;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0428c|Rv0428c|transcript|Rv0428c|protein_coding|1/1|c.446G>A|p.Gly149Asp|446/909|446/909|149/302||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:982:-88.6757,-8.42884,0
Chromosome	517411	.	G	A	951.814	.	AB=0;AO=30;DP=31;QA=1088;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0428c|Rv0428c|transcript|Rv0428c|protein_coding|1/1|c.393C>T|p.Arg131Arg|393/909|393/909|131/302||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:30:1088:-98.0682,-9.0309,0
Chromosome	519185	.	G	T	822.384	.	AB=0;AO=26;DP=26;QA=942;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0431|Rv0431|transcript|Rv0431|protein_coding|1/1|c.113G>T|p.Gly38Val|113/495|113/495|38/164||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:942:-85.0885,-7.82678,0
Chromosome	522081	.	G	A	454.143	.	AB=0;AO=15;DP=15;QA=527;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0434|Rv0434|transcript|Rv0434|protein_coding|1/1|c.568G>A|p.Ala190Thr|568/654|568/654|190/217||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:527:-47.7532,-4.51545,0
Chromosome	527316	.	G	C	980.814	.	AB=0;AO=30;DP=30;QA=1121;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|moeA2|Rv0438c|transcript|Rv0438c|protein_coding|1/1|c.45C>G|p.Ile15Met|45/1218|45/1218|15/405||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1121:-101.196,-9.0309,0
Chromosome	528354	.	A	C	685.842	.	AB=0;AO=22;DP=22;QA=789;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv0439c-groEL2|Rv0439c-Rv0440|intergenic_region|Rv0439c-Rv0440|||n.528354A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:789:-71.326,-6.62266,0
Chromosome	534427	.	A	T	729.61	.	AB=0;AO=24;DP=24;QA=844;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|sigK-Rv0446c|Rv0445c-Rv0446c|intergenic_region|Rv0445c-Rv0446c|||n.534427A>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:844:-76.2667,-7.22472,0
Chromosome	546357	.	G	A	837.647	.	AB=0;AO=28;DP=28;QA=970;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|echA2|Rv0456c|transcript|Rv0456c|protein_coding|1/1|c.447C>T|p.Thr149Thr|447/915|447/915|149/304||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:970:-87.5924,-8.42884,0
Chromosome	546914	.	G	A	614.547	.	AB=0;AO=20;DP=20;QA=711;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|echA2-mazF1|Rv0456c-Rv0456A|intergenic_region|Rv0456c-Rv0456A|||n.546914G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:711:-64.3017,-6.0206,0
Chromosome	555991	.	G	A	427.151	.	AB=0;AO=14;DP=14;QA=505;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0465c|Rv0465c|transcript|Rv0465c|protein_coding|1/1|c.316C>T|p.Arg106Cys|316/1425|316/1425|106/474||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:505:-45.7841,-4.21442,0
Chromosome	565404	.	T	G	833.53	.	AB=0;AO=27;DP=27;QA=958;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv0474|Rv0474|transcript|Rv0474|protein_coding|1/1|c.384T>G|p.Arg128Arg|384/423|384/423|128/140||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:958:-86.5231,-8.12781,0
Chromosome	573384	.	G	T	621.432	.	AB=0;AO=20;DP=20;QA=713;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0484c|Rv0484c|transcript|Rv0484c|protein_coding|1/1|c.418C>A|p.Leu140Ile|418/756|418/756|140/251||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:713:-64.4879,-6.0206,0
Chromosome	580772	.	TGGGGGCACCACCCGCTTGCGGGGGA	AG	572.081	.	AB=0;AO=18;DP=18;QA=661;QR=0;RO=0;TYPE=complex;ANN=AG|intergenic_region|MODIFIER|senX3-regX3|Rv0490-Rv0491|intergenic_region|Rv0490-Rv0491|||n.580772_580797delTGGGGGCACCACCCGCTTGCGGGGGAinsAG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:661:-59.8171,-5.41854,0
Chromosome	584171	.	C	T	634.579	.	AB=0;AO=20;DP=20;QA=739;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0493c|Rv0493c|transcript|Rv0493c|protein_coding|1/1|c.520G>A|p.Gly174Ser|520/990|520/990|174/329||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:739:-66.8374,-6.0206,0
Chromosome	584511	.	T	G	357.585	.	AB=0;AO=13;DP=13;QA=440;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv0493c|Rv0493c|transcript|Rv0493c|protein_coding|1/1|c.180A>C|p.Thr60Thr|180/990|180/990|60/329||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:440:-39.9157,-3.91339,0
Chromosome	590763	.	C	G	429.749	.	AB=0;AO=14;DP=14;QA=505;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|proC|Rv0500|transcript|Rv0500|protein_coding|1/1|c.681C>G|p.Asp227Glu|681/888|681/888|227/295||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:505:-45.7807,-4.21442,0
Chromosome	595321	.	T	G	789.339	.	AB=0;AO=25;DP=25;QA=905;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv0504c-serB1|Rv0504c-Rv0505c|intergenic_region|Rv0504c-Rv0505c|||n.595321T>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:905:-81.7664,-7.52575,0
Chromosome	595399	.	AT	A	470.094	.	AB=0;AO=16;DP=16;QA=566;QR=0;RO=0;TYPE=del;ANN=A|intergenic_region|MODIFIER|Rv0504c-serB1|Rv0504c-Rv0505c|intergenic_region|Rv0504c-Rv0505c|||n.595400delT||||||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:566:-51.2629,-4.81648,0
Chromosome	599165	.	A	C	731.549	.	AB=0;AO=23;DP=23;QA=843;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|mmpL2|Rv0507|transcript|Rv0507|protein_coding|1/1|c.1967A>C|p.Glu656Ala|1967/2907|1967/2907|656/968||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:843:-76.1921,-6.92369,0
Chromosome	599868	.	G	A	1099.19	.	AB=0;AO=35;DP=35;QA=1249;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|mmpL2|Rv0507|transcript|Rv0507|protein_coding|1/1|c.2670G>A|p.Arg890Arg|2670/2907|2670/2907|890/968||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1249:-112.702,-10.5361,0
Chromosome	628895	.	G	A	746.246	.	AB=0;AO=24;DP=24;QA=853;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0537c|Rv0537c|transcript|Rv0537c|protein_coding|1/1|c.837C>T|p.Phe279Phe|837/1434|837/1434|279/477||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:853:-77.0722,-7.22472,0
Chromosome	648856	.	C	T	696.663	.	AB=0;AO=24;DP=24;QA=798;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|mgtA|Rv0557|transcript|Rv0557|protein_coding|1/1|c.321C>T|p.Gly107Gly|321/1137|321/1137|107/378||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:798:-72.1139,-7.22472,0
Chromosome	649436	.	CCGGA	C	862.502	.	AB=0;AO=30;DP=30;QA=1000;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|mgtA|Rv0557|transcript|Rv0557|protein_coding|1/1|c.904_907delGACG|p.Asp302fs|904/1137|904/1137|302/378||INFO_REALIGN_3_PRIME;LOF=(mgtA|Rv0557|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1000:-90.2873,-9.0309,0
Chromosome	655986	.	G	T	738.585	.	AB=0;AO=24;DP=24;QA=846;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|gpdA1-Rv0565c|Rv0564c-Rv0565c|intergenic_region|Rv0564c-Rv0565c|||n.655986G>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:846:-76.4456,-7.22472,0
Chromosome	657269	.	A	G	504.462	.	AB=0;AO=17;DP=17;QA=588;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0565c|Rv0565c|transcript|Rv0565c|protein_coding|1/1|c.202T>C|p.Ser68Pro|202/1461|202/1461|68/486||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:588:-53.2356,-5.11751,0
Chromosome	657578	.	G	A	505.833	.	AB=0;AO=16;DP=16;QA=590;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0566c|Rv0566c|transcript|Rv0566c|protein_coding|1/1|c.462C>T|p.Asp154Asp|462/492|462/492|154/163||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:590:-53.4305,-4.81648,0
Chromosome	659341	.	C	T	275.512	.	AB=0;AO=10;DP=10;QA=333;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0567-cyp135B1|Rv0567-Rv0568|intergenic_region|Rv0567-Rv0568|||n.659341C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:333:-30.2845,-3.0103,0
Chromosome	662911	.	C	T	989.354	.	AB=0;AO=31;DP=31;QA=1128;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|nrdZ|Rv0570|transcript|Rv0570|protein_coding|1/1|c.1617C>T|p.Ala539Ala|1617/2079|1617/2079|539/692||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1128:-101.825,-9.33193,0
Chromosome	670545	.	A	G	747.641	.	AB=0;AO=24;DP=24;QA=856;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0576|Rv0576|transcript|Rv0576|protein_coding|1/1|c.698A>G|p.His233Arg|698/1305|698/1305|233/434||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:856:-77.3511,-7.22472,0
Chromosome	684290	.	G	A	955.922	.	AB=0;AO=30;DP=30;QA=1096;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv0585c-mce2R|Rv0585c-Rv0586|intergenic_region|Rv0585c-Rv0586|||n.684290G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1096:-98.9381,-9.0309,0
Chromosome	686655	.	C	T	854.925	.	AB=0;AO=28;DP=30;QA=1045;QR=73;RO=2;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0588|Rv0588|transcript|Rv0588|protein_coding|1/1|c.728C>T|p.Thr243Ile|728/888|728/888|243/295||	GT:DP:RO:QR:AO:QA:GL	1/1:30:2:73:28:1045:-87.4279,-2.0996,0
Chromosome	690248	.	A	C	812.27	.	AB=0;AO=27;DP=27;QA=928;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|mce2C|Rv0591|transcript|Rv0591|protein_coding|1/1|c.1190A>C|p.Asn397Thr|1190/1446|1190/1446|397/481||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:928:-83.8278,-8.12781,0
Chromosome	690450	.	C	A	373.557	.	AB=0;AO=13;DP=13;QA=449;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|mce2C|Rv0591|transcript|Rv0591|protein_coding|1/1|c.1392C>A|p.Ala464Ala|1392/1446|1392/1446|464/481||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:449:-40.7348,-3.91339,0
Chromosome	698828	.	G	A	575.62	.	AB=0;AO=19;DP=19;QA=668;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0601c|Rv0601c|transcript|Rv0601c|protein_coding|1/1|c.167C>T|p.Ala56Val|167/471|167/471|56/156||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:668:-60.4377,-5.71957,0
Chromosome	700776	.	C	T	887.582	.	AB=0;AO=28;DP=28;QA=1015;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|lpqO|Rv0604|transcript|Rv0604|protein_coding|1/1|c.538C>T|p.Pro180Ser|538/951|538/951|180/316||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1015:-91.6562,-8.42884,0
Chromosome	705602	.	C	T	577.158	.	AB=0;AO=18;DP=18;QA=675;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0610c|Rv0610c|transcript|Rv0610c|protein_coding|1/1|c.308G>A|p.Ser103Asn|308/1158|308/1158|103/385||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:675:-61.083,-5.41854,0
Chromosome	713310	.	C	T	670.732	.	AB=0;AO=23;DP=23;QA=787;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|galK|Rv0620|transcript|Rv0620|protein_coding|1/1|c.595C>T|p.Arg199Cys|595/1092|595/1092|199/363||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:787:-71.1278,-6.92369,0
Chromosome	715266	.	G	A	437.538	.	AB=0;AO=14;DP=14;QA=507;QR=0;RO=0;TYPE=snp;ANN=A|stop_gained&splice_region_variant|HIGH|Rv0621|Rv0621|transcript|Rv0621|protein_coding|1/1|c.1065G>A|p.Trp355*|1065/1065|1065/1065|355/354||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:507:-45.9644,-4.21442,0
Chromosome	717588	.	G	A	1256.64	.	AB=0;AO=40;DP=40;QA=1438;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0625c|Rv0625c|transcript|Rv0625c|protein_coding|1/1|c.306C>T|p.Val102Val|306/741|306/741|102/246||	GT:DP:RO:QR:AO:QA:GL	1/1:40:0:0:40:1438:-129.704,-12.0412,0
Chromosome	721410	.	T	C	784.147	.	AB=0;AO=26;DP=26;QA=910;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|recD|Rv0629c|transcript|Rv0629c|protein_coding|1/1|c.323A>G|p.Asp108Gly|323/1728|323/1728|108/575||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:910:-82.2041,-7.82678,0
Chromosome	726816	.	G	C	459.629	.	AB=0;AO=16;DP=16;QA=546;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|recC|Rv0631c|transcript|Rv0631c|protein_coding|1/1|c.1491C>G|p.Phe497Leu|1491/3294|1491/3294|497/1097||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:546:-49.4536,-4.81648,0
Chromosome	728556	.	GC	G	758.419	.	AB=0;AO=26;DP=26;QA=874;QR=0;RO=0;TYPE=del;ANN=G|intergenic_region|MODIFIER|recC-echA3|Rv0631c-Rv0632c|intergenic_region|Rv0631c-Rv0632c|||n.728557delC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:874:-78.9546,-7.82678,0
Chromosome	746045	.	G	C	309.063	.	AB=0;AO=11;DP=11;QA=381;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv0648|Rv0648|transcript|Rv0648|protein_coding|1/1|c.3327G>C|p.Leu1109Leu|3327/3648|3327/3648|1109/1215||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:381:-34.6158,-3.31133,0
Chromosome	757182	.	G	A	995.555	.	AB=0;AO=32;DP=32;QA=1139;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|atsD|Rv0663|transcript|Rv0663|protein_coding|1/1|c.1046G>A|p.Gly349Asp|1046/2364|1046/2364|349/787||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1139:-102.807,-9.63296,0
Chromosome	761109	.	G	T	704.156	.	AB=0;AO=23;DP=23;QA=807;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|rpoB|Rv0667|transcript|Rv0667|protein_coding|1/1|c.1303G>T|p.Asp435Tyr|1303/3519|1303/3519|435/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:807:-72.9388,-6.92369,0
Chromosome	763031	.	C	T	802.077	.	AB=0;AO=25;DP=25;QA=917;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|rpoB|Rv0667|transcript|Rv0667|protein_coding|1/1|c.3225C>T|p.Ala1075Ala|3225/3519|3225/3519|1075/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:917:-82.8385,-7.52575,0
Chromosome	765150	.	G	A	705.296	.	AB=0;AO=22;DP=22;QA=808;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|rpoC|Rv0668|transcript|Rv0668|protein_coding|1/1|c.1781G>A|p.Gly594Glu|1781/3951|1781/3951|594/1316||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:808:-73.0417,-6.62266,0
Chromosome	776100	.	A	G	1065.25	.	AB=0;AO=34;DP=34;QA=1214;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mmpL5|Rv0676c|transcript|Rv0676c|protein_coding|1/1|c.2381T>C|p.Ile794Thr|2381/2895|2381/2895|794/964||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1214:-109.552,-10.235,0
Chromosome	782246	.	G	A	716.625	.	AB=0;AO=23;DP=23;QA=820;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|rpsG|Rv0683|transcript|Rv0683|protein_coding|1/1|c.313G>A|p.Val105Ile|313/471|313/471|105/156||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:820:-74.1132,-6.92369,0
Chromosome	788259	.	G	T	578.382	.	AB=0;AO=19;DP=19;QA=683;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0688|Rv0688|transcript|Rv0688|protein_coding|1/1|c.320G>T|p.Gly107Val|320/1221|320/1221|107/406||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:683:-61.7956,-5.71957,0
Chromosome	794480	.	CG	C	421.107	.	AB=0;AO=14;DP=15;QA=490;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv0694|Rv0694|transcript|Rv0694|protein_coding|1/1|c.1149delG|p.Phe384fs|1149/1191|1149/1191|383/396||INFO_REALIGN_3_PRIME	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:14:490:-44.2053,-4.21442,0
Chromosome	800219	.	T	C	1224.65	.	AB=0;AO=40;DP=40;QA=1401;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv0699-rpsJ|Rv0699-Rv0700|intergenic_region|Rv0699-Rv0700|||n.800219T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:40:0:0:40:1401:-126.37,-12.0412,0
Chromosome	815236	.	C	T	927.539	.	AB=0;AO=29;DP=29;QA=1061;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|rplO|Rv0723|transcript|Rv0723|protein_coding|1/1|c.47C>T|p.Thr16Ile|47/441|47/441|16/146||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1061:-95.7981,-8.72987,0
Chromosome	815851	.	G	A	499.82	.	AB=0;AO=16;DP=16;QA=581;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|sppA|Rv0724|transcript|Rv0724|protein_coding|1/1|c.189G>A|p.Arg63Arg|189/1872|189/1872|63/623||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:581:-52.6231,-4.81648,0
Chromosome	820752	.	T	C	393.682	.	AB=0;AO=13;DP=13;QA=462;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|serA2|Rv0728c|transcript|Rv0728c|protein_coding|1/1|c.725A>G|p.His242Arg|725/981|725/981|242/326||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:462:-41.91,-3.91339,0
Chromosome	821907	.	C	T	591.125	.	AB=0;AO=18;DP=18;QA=678;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|xylB|Rv0729|transcript|Rv0729|protein_coding|1/1|c.401C>T|p.Pro134Leu|401/1347|401/1347|134/448||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:678:-61.3535,-5.41854,0
Chromosome	828176	.	G	C	924.778	.	AB=0;AO=29;DP=29;QA=1056;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|rslA|Rv0736|transcript|Rv0736|protein_coding|1/1|c.37G>C|p.Asp13His|37/753|37/753|13/250||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1056:-95.3475,-8.72987,0
Chromosome	832201	.	T	C	306.955	.	AB=0;AO=10;DP=10;QA=362;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv0740|Rv0740|transcript|Rv0740|protein_coding|1/1|c.426T>C|p.Asp142Asp|426/528|426/528|142/175||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:362:-32.9236,-3.0103,0
Chromosome	832246	.	G	A	379.759	.	AB=0;AO=13;DP=13;QA=448;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0740|Rv0740|transcript|Rv0740|protein_coding|1/1|c.471G>A|p.Gln157Gln|471/528|471/528|157/175||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:448:-40.6426,-3.91339,0
Chromosome	841924	.	C	T	747.812	.	AB=0;AO=23;DP=23;QA=857;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv0749A-Rv0750|Rv0749A-Rv0750|intergenic_region|Rv0749A-Rv0750|||n.841924C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:857:-77.4505,-6.92369,0
Chromosome	847995	.	C	T	916.098	.	AB=0;AO=29;DP=29;QA=1055;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|PE_PGRS11-PPE12|Rv0754-Rv0755c|intergenic_region|Rv0754-Rv0755c|||n.847995C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1055:-95.252,-8.72987,0
Chromosome	848407	.	T	C	455.331	.	AB=0;AO=14;DP=14;QA=528;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|PPE12|Rv0755c|transcript|Rv0755c|protein_coding|1/1|c.1634A>G|p.Lys545Arg|1634/1938|1634/1938|545/645||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:528:-47.8617,-4.21442,0
Chromosome	850591	.	C	T	1066.5	.	AB=0;AO=36;DP=36;QA=1217;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|PPE12-thrV|Rv0755c-Rvnt09|intergenic_region|Rv0755c-Rvnt09|||n.850591C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1217:-109.806,-10.8371,0
Chromosome	851133	.	T	G	510.194	.	AB=0;AO=17;DP=17;QA=591;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0756c|Rv0756c|transcript|Rv0756c|protein_coding|1/1|c.334A>C|p.Thr112Pro|334/726|334/726|112/241||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:591:-53.5078,-5.11751,0
Chromosome	854252	.	GC	G	454.449	.	AB=0;AO=16;DP=17;QA=556;QR=36;RO=1;TYPE=del;ANN=G|intergenic_region|MODIFIER|Rv0759c-Rv0760c|Rv0759c-Rv0760c|intergenic_region|Rv0759c-Rv0760c|||n.854253delC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:1:36:16:556:-46.7649,-1.51924,0
Chromosome	864184	.	G	A	551.573	.	AB=0;AO=20;DP=22;QA=694;QR=61;RO=2;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0771|Rv0771|transcript|Rv0771|protein_coding|1/1|c.45G>A|p.Glu15Glu|45/435|45/435|15/144||	GT:DP:RO:QR:AO:QA:GL	1/1:22:2:61:20:694:-56.9762,-0.829825,0
Chromosome	865737	.	C	T	606.232	.	AB=0;AO=19;DP=19;QA=708;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|purD|Rv0772|transcript|Rv0772|protein_coding|1/1|c.1152C>T|p.Ala384Ala|1152/1269|1152/1269|384/422||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:708:-64.0485,-5.71957,0
Chromosome	868488	.	G	A	431.687	.	AB=0;AO=15;DP=15;QA=540;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0775|Rv0775|transcript|Rv0775|protein_coding|1/1|c.82G>A|p.Glu28Lys|82/624|82/624|28/207||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:540:-48.9263,-4.51545,0
Chromosome	869440	.	C	T	748.213	.	AB=0;AO=23;DP=23;QA=855;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0776c|Rv0776c|transcript|Rv0776c|protein_coding|1/1|c.324G>A|p.Leu108Leu|324/780|324/780|108/259||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:855:-77.2719,-6.92369,0
Chromosome	871271	.	C	A	772.357	.	AB=0;AO=25;DP=25;QA=884;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|purB|Rv0777|transcript|Rv0777|protein_coding|1/1|c.1264C>A|p.Pro422Thr|1264/1419|1264/1419|422/472||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:884:-79.8657,-7.52575,0
Chromosome	872108	.	C	G	338.385	.	AB=0;AO=11;DP=11;QA=397;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|cyp126|Rv0778|transcript|Rv0778|protein_coding|1/1|c.678C>G|p.Ala226Ala|678/1245|678/1245|226/414||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:397:-36.0708,-3.31133,0
Chromosome	874835	.	C	CCG	821.6	.	AB=0;AO=29;DP=30;QA=970;QR=0;RO=0;TYPE=ins;ANN=CCG|intergenic_region|MODIFIER|purC-emrB|Rv0780-Rv0783c|intergenic_region|Rv0780-Rv0783c|||n.874835_874836insCG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:29:970:-87.3156,-8.72987,0
Chromosome	877224	.	C	A	1134.72	.	AB=0;AO=35;DP=35;QA=1289;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|emrB|Rv0783c|transcript|Rv0783c|protein_coding|1/1|c.1217G>T|p.Gly406Val|1217/1623|1217/1623|406/540||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1289:-116.303,-10.5361,0
Chromosome	880935	.	C	T	691.224	.	AB=0;AO=24;DP=25;QA=809;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0785|Rv0785|transcript|Rv0785|protein_coding|1/1|c.1596C>T|p.Gly532Gly|1596/1701|1596/1701|532/566||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:24:809:-72.8484,-7.22472,0
Chromosome	894888	.	C	T	796.895	.	AB=0;AO=25;DP=25;QA=909;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0801|Rv0801|transcript|Rv0801|protein_coding|1/1|c.258C>T|p.Ser86Ser|258/348|258/348|86/115||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:909:-82.1186,-7.52575,0
Chromosome	896356	.	C	T	451.751	.	AB=0;AO=14;DP=14;QA=528;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|purL|Rv0803|transcript|Rv0803|protein_coding|1/1|c.537C>T|p.Thr179Thr|537/2265|537/2265|179/754||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:528:-47.8629,-4.21442,0
Chromosome	897209	.	G	C	592.761	.	AB=0;AO=19;DP=19;QA=685;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|purL|Rv0803|transcript|Rv0803|protein_coding|1/1|c.1390G>C|p.Glu464Gln|1390/2265|1390/2265|464/754||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:685:-61.9757,-5.71957,0
Chromosome	902413	.	C	T	664.05	.	AB=0;AO=21;DP=21;QA=779;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|purF|Rv0808|transcript|Rv0808|protein_coding|1/1|c.303C>T|p.Val101Val|303/1584|303/1584|101/527||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:779:-70.4326,-6.32163,0
Chromosome	911261	.	C	T	530.07	.	AB=0;AO=18;DP=19;QA=634;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0818|Rv0818|transcript|Rv0818|protein_coding|1/1|c.290C>T|p.Pro97Leu|290/768|290/768|97/255||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:18:634:-57.2071,-5.41854,0
Chromosome	913274	.	G	C	1017.16	.	AB=0;AO=32;DP=32;QA=1156;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|phoT|Rv0820|transcript|Rv0820|protein_coding|1/1|c.549G>C|p.Ser183Ser|549/777|549/777|183/258||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1156:-104.331,-9.63296,0
Chromosome	916046	.	G	T	306.957	.	AB=0;AO=10;DP=10;QA=362;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0822c|Rv0822c|transcript|Rv0822c|protein_coding|1/1|c.266C>A|p.Pro89His|266/2055|266/2055|89/684||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:362:-32.9238,-3.0103,0
Chromosome	918316	.	T	C	682.542	.	AB=0;AO=22;DP=22;QA=788;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|desA1|Rv0824c|transcript|Rv0824c|protein_coding|1/1|c.435A>G|p.Gln145Gln|435/1017|435/1017|145/338||,C|intragenic_variant|MODIFIER|ASdes|RVnc0002|gene_variant|RVnc0002|||n.918316T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:788:-71.2312,-6.62266,0
Chromosome	919574	.	T	C	819.58	.	AB=0;AO=26;DP=26;QA=936;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv0825c-Rv0826|Rv0825c-Rv0826|intergenic_region|Rv0825c-Rv0826|||n.919574T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:936:-84.5485,-7.82678,0
Chromosome	920747	.	G	A	450.039	.	AB=0;AO=14;DP=14;QA=530;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|kmtR|Rv0827c|transcript|Rv0827c|protein_coding|1/1|c.387C>T|p.Val129Val|387/393|387/393|129/130||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:530:-48.0438,-4.21442,0
Chromosome	923065	.	T	A	915.302	.	AB=0;AO=29;DP=29;QA=1054;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0831c|Rv0831c|transcript|Rv0831c|protein_coding|1/1|c.645A>T|p.Gly215Gly|645/816|645/816|215/271||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1054:-95.164,-8.72987,0
Chromosome	931123	.	C	T	867.746	.	AB=0;AO=27;DP=27;QA=989;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|lpqQ|Rv0835|transcript|Rv0835|protein_coding|1/1|c.171C>T|p.Tyr57Tyr|171/645|171/645|57/214||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:989:-89.3133,-8.12781,0
Chromosome	931417	.	C	T	561.903	.	AB=0;AO=21;DP=21;QA=655;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|lpqQ|Rv0835|transcript|Rv0835|protein_coding|1/1|c.465C>T|p.Pro155Pro|465/645|465/645|155/214||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:655:-59.2337,-6.32163,0
Chromosome	932280	.	C	T	658.635	.	AB=0;AO=21;DP=21;QA=755;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained&splice_region_variant|HIGH|Rv0836c|Rv0836c|transcript|Rv0836c|protein_coding|1/1|c.653G>A|p.Trp218*|653/654|653/654|218/217||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:755:-68.2653,-6.32163,0
Chromosome	933699	.	T	G	738.037	.	AB=0;AO=23;DP=23;QA=847;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv0837c|Rv0837c|transcript|Rv0837c|protein_coding|1/1|c.333A>C|p.Gly111Gly|333/1029|333/1029|111/342||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:847:-76.5455,-6.92369,0
Chromosome	934230	.	G	C	396.925	.	AB=0;AO=13;DP=13;QA=479;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv0837c-lpqR|Rv0837c-Rv0838|intergenic_region|Rv0837c-Rv0838|||n.934230G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:479:-43.4518,-3.91339,0
Chromosome	934611	.	T	G	925.15	.	AB=0;AO=30;DP=30;QA=1063;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv0837c-lpqR|Rv0837c-Rv0838|intergenic_region|Rv0837c-Rv0838|||n.934611T>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1063:-95.9702,-9.0309,0
Chromosome	938246	.	G	A	565.752	.	AB=0;AO=18;DP=18;QA=654;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0842|Rv0842|transcript|Rv0842|protein_coding|1/1|c.135G>A|p.Leu45Leu|135/1293|135/1293|45/430||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:654:-59.1842,-5.41854,0
Chromosome	941845	.	A	C	621.432	.	AB=0;AO=20;DP=20;QA=730;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0845|Rv0845|transcript|Rv0845|protein_coding|1/1|c.656A>C|p.Glu219Ala|656/1278|656/1278|219/425||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:730:-66.0249,-6.0206,0
Chromosome	948294	.	C	T	903.217	.	AB=0;AO=28;DP=28;QA=1049;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0851c|Rv0851c|transcript|Rv0851c|protein_coding|1/1|c.175G>A|p.Gly59Ser|175/828|175/828|59/275||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1049:-94.7198,-8.42884,0
Chromosome	950230	.	C	T	898.57	.	AB=0;AO=29;DP=29;QA=1029;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|pdc|Rv0853c|transcript|Rv0853c|protein_coding|1/1|c.889G>A|p.Asp297Asn|889/1683|889/1683|297/560||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1029:-92.9028,-8.72987,0
Chromosome	951142	.	A	C	923.025	.	AB=0;AO=28;DP=28;QA=1053;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|pdc-Rv0854|Rv0853c-Rv0854|intergenic_region|Rv0853c-Rv0854|||n.951142A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1053:-95.0805,-8.42884,0
Chromosome	960367	.	G	A	844.012	.	AB=0;AO=27;DP=27;QA=971;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0862c|Rv0862c|transcript|Rv0862c|protein_coding|1/1|c.2246C>T|p.Ser749Leu|2246/2271|2246/2271|749/756||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:971:-87.6922,-8.12781,0
Chromosome	978373	.	T	C	714.654	.	AB=0;AO=24;DP=24;QA=829;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|PPE13-Rv0879c|Rv0878c-Rv0879c|intergenic_region|Rv0878c-Rv0879c|||n.978373T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:829:-74.9106,-7.22472,0
Chromosome	979859	.	T	C	1136.98	.	AB=0;AO=36;DP=36;QA=1293;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv0881|Rv0881|transcript|Rv0881|protein_coding|1/1|c.498T>C|p.Ala166Ala|498/867|498/867|166/288||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1293:-116.665,-10.8371,0
Chromosome	983485	.	T	G	643.807	.	AB=0;AO=21;DP=21;QA=759;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0885|Rv0885|transcript|Rv0885|protein_coding|1/1|c.724T>G|p.Ser242Ala|724/1023|724/1023|242/340||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:759:-68.6321,-6.32163,0
Chromosome	996982	.	G	A	728.69	.	AB=0;AO=23;DP=23;QA=835;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0894|Rv0894|transcript|Rv0894|protein_coding|1/1|c.459G>A|p.Ala153Ala|459/1182|459/1182|153/393||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:835:-75.4657,-6.92369,0
Chromosome	1010204	.	C	CG	773.038	.	AB=0;AO=25;DP=27;QA=887;QR=0;RO=0;TYPE=ins;ANN=CG|frameshift_variant|HIGH|Rv0907|Rv0907|transcript|Rv0907|protein_coding|1/1|c.71dupG|p.Cys25fs|72/1599|72/1599|24/532||INFO_REALIGN_3_PRIME	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:25:887:-79.8669,-7.52575,0
Chromosome	1014815	.	G	T	1191.56	.	AB=0;AO=37;DP=37;QA=1352;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0909|Rv0909|transcript|Rv0909|protein_coding|1/1|c.135G>T|p.Gln45His|135/180|135/180|45/59||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1352:-121.966,-11.1381,0
Chromosome	1024346	.	G	A	780.523	.	AB=0;AO=25;DP=25;QA=906;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0918|Rv0918|transcript|Rv0918|protein_coding|1/1|c.136G>A|p.Gly46Ser|136/477|136/477|46/158||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:906:-81.8454,-7.52575,0
Chromosome	1028944	.	C	T	666.753	.	AB=0;AO=21;DP=21;QA=772;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0922|Rv0922|transcript|Rv0922|protein_coding|1/1|c.1260C>T|p.Tyr420Tyr|1260/1653|1260/1653|420/550||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:772:-69.7979,-6.32163,0
Chromosome	1040706	.	C	A	693.874	.	AB=0;AO=23;DP=23;QA=798;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|pstS2|Rv0932c|transcript|Rv0932c|protein_coding|1/1|c.343G>T|p.Ala115Ser|343/1113|343/1113|115/370||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:798:-72.1293,-6.92369,0
Chromosome	1049508	.	C	T	494.037	.	AB=0;AO=16;DP=16;QA=584;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0939|Rv0939|transcript|Rv0939|protein_coding|1/1|c.1097C>T|p.Ala366Val|1097/1935|1097/1935|366/644||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:584:-52.8943,-4.81648,0
Chromosome	1054784	.	G	C	1116.47	.	AB=0;AO=35;DP=35;QA=1273;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0945|Rv0945|transcript|Rv0945|protein_coding|1/1|c.538G>C|p.Gly180Arg|538/762|538/762|180/253||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1273:-114.869,-10.5361,0
Chromosome	1063765	.	A	G	882.54	.	AB=0;AO=30;DP=30;QA=1026;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|sucD|Rv0952|transcript|Rv0952|protein_coding|1/1|c.626A>G|p.Lys209Arg|626/912|626/912|209/303||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1026:-92.6351,-9.0309,0
Chromosome	1080192	.	A	G	376.099	.	AB=0;AO=13;DP=13;QA=447;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ctpV|Rv0969|transcript|Rv0969|protein_coding|1/1|c.1450A>G|p.Asn484Asp|1450/2313|1450/2313|484/770||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:447:-40.5496,-3.91339,0
Chromosome	1090292	.	C	G	408.297	.	AB=0;AO=14;DP=14;QA=502;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv0976c-PE_PGRS16|Rv0976c-Rv0977|intergenic_region|Rv0976c-Rv0977|||n.1090292C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:502:-45.513,-4.21442,0
Chromosome	1096633	.	T	G	593.649	.	AB=0;AO=19;DP=19;QA=705;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|PE_PGRS18-mprA|Rv0980c-Rv0981|intergenic_region|Rv0980c-Rv0981|||n.1096633T>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:705:-63.7804,-5.71957,0
Chromosome	1097023	.	A	G	725.41	.	AB=0;AO=24;DP=24;QA=844;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mprA|Rv0981|transcript|Rv0981|protein_coding|1/1|c.202A>G|p.Ser68Gly|202/687|202/687|68/228||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:844:-76.267,-7.22472,0
Chromosome	1098523	.	A	T	502.84	.	AB=0;AO=16;DP=16;QA=588;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|mprB|Rv0982|transcript|Rv0982|protein_coding|1/1|c.1016A>T|p.His339Leu|1016/1515|1016/1515|339/504||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:588:-53.2542,-4.81648,0
Chromosome	1102788	.	G	T	550.411	.	AB=0;AO=18;DP=18;QA=634;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0987|Rv0987|transcript|Rv0987|protein_coding|1/1|c.247G>T|p.Val83Phe|247/2568|247/2568|83/855||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:634:-57.3735,-5.41854,0
Chromosome	1104690	.	G	T	384.874	.	AB=0;AO=12;DP=12;QA=453;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0987|Rv0987|transcript|Rv0987|protein_coding|1/1|c.2149G>T|p.Val717Phe|2149/2568|2149/2568|717/855||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:453:-41.1176,-3.61236,0
Chromosome	1105284	.	A	G	881.324	.	AB=0;AO=28;DP=28;QA=1004;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0988|Rv0988|transcript|Rv0988|protein_coding|1/1|c.169A>G|p.Ile57Val|169/1161|169/1161|57/386||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1004:-90.6689,-8.42884,0
Chromosome	1106877	.	T	C	737.361	.	AB=0;AO=25;DP=27;QA=914;QR=73;RO=2;TYPE=snp;ANN=C|missense_variant|MODERATE|grcC2|Rv0989c|transcript|Rv0989c|protein_coding|1/1|c.506A>G|p.Tyr169Cys|506/978|506/978|169/325||	GT:DP:RO:QR:AO:QA:GL	1/1:27:2:73:25:914:-75.6431,-1.19651,0
Chromosome	1107940	.	C	A	677.538	.	AB=0;AO=24;DP=24;QA=792;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv0990c|Rv0990c|transcript|Rv0990c|protein_coding|1/1|c.160G>T|p.Ala54Ser|160/657|160/657|54/218||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:792:-71.5743,-7.22472,0
Chromosome	1109163	.	G	C	590.911	.	AB=0;AO=19;DP=19;QA=681;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv0992c|Rv0992c|transcript|Rv0992c|protein_coding|1/1|c.9C>G|p.Ile3Met|9/594|9/594|3/197||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:681:-61.6163,-5.71957,0
Chromosome	1110956	.	G	T	389.098	.	AB=0;AO=14;DP=14;QA=463;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|moeA1|Rv0994|transcript|Rv0994|protein_coding|1/1|c.688G>T|p.Gly230Cys|688/1281|688/1281|230/426||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:463:-41.9789,-4.21442,0
Chromosome	1113290	.	C	G	837.929	.	AB=0;AO=27;DP=27;QA=967;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv0996|Rv0996|transcript|Rv0996|protein_coding|1/1|c.907C>G|p.Gln303Glu|907/1077|907/1077|303/358||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:967:-87.3391,-8.12781,0
Chromosome	1123597	.	G	A	964.208	.	AB=0;AO=31;DP=31;QA=1102;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1005c|Rv1005c|transcript|Rv1005c|protein_coding|1/1|c.2C>T|p.Ser1Leu|2/1377|2/1377|1/458||WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1102:-99.4734,-9.33193,0
Chromosome	1131300	.	A	G	531.987	.	AB=0;AO=17;DP=17;QA=623;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1012|Rv1012|transcript|Rv1012|protein_coding|1/1|c.173A>G|p.Asn58Ser|173/294|173/294|58/97||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:623:-56.4031,-5.11751,0
Chromosome	1144585	.	G	A	570.927	.	AB=0;AO=19;DP=19;QA=658;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|eno|Rv1023|transcript|Rv1023|protein_coding|1/1|c.22G>A|p.Gly8Arg|22/1290|22/1290|8/429||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:658:-59.529,-5.71957,0
Chromosome	1148255	.	GCCGG	ACCGA	728.737	.	AB=0;AO=24;DP=24;QA=835;QR=0;RO=0;TYPE=complex;ANN=ACCGA|intergenic_region|MODIFIER|Rv1026-kdpE|Rv1026-Rv1027c|intergenic_region|Rv1026-Rv1027c|||n.1148255_1148259delGCCGGinsACCGA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:835:-75.4607,-7.22472,0
Chromosome	1159854	.	C	T	527.531	.	AB=0;AO=17;DP=17;QA=608;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|trcR-esxI|Rv1033c-Rv1037c|intergenic_region|Rv1033c-Rv1037c|||n.1159854C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:608:-55.0452,-5.11751,0
Chromosome	1164361	.	G	A	713.679	.	AB=0;AO=22;DP=22;QA=819;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|PE8-Rv1041c|Rv1040c-Rv1041c|intergenic_region|Rv1040c-Rv1041c|||n.1164361G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:819:-74.0317,-6.62266,0
Chromosome	1164571	.	A	G	931.69	.	AB=0;AO=30;DP=30;QA=1064;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|PE8-Rv1041c|Rv1040c-Rv1041c|intergenic_region|Rv1040c-Rv1041c|||n.1164571A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1064:-96.0557,-9.0309,0
Chromosome	1168718	.	T	TC	882.508	.	AB=0;AO=30;DP=30;QA=1026;QR=0;RO=0;TYPE=ins;ANN=TC|intergenic_region|MODIFIER|Rv1045-Rv1047|Rv1045-Rv1047|intergenic_region|Rv1045-Rv1047|||n.1168718_1168719insC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1026:-92.6319,-9.0309,0
Chromosome	1174515	.	C	T	609.887	.	AB=0;AO=20;DP=20;QA=704;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1051c|Rv1051c|transcript|Rv1051c|protein_coding|1/1|c.186G>A|p.Ala62Ala|186/756|186/756|62/251||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:704:-63.6693,-6.0206,0
Chromosome	1203824	.	C	T	668.868	.	AB=0;AO=21;DP=21;QA=769;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1078|Rv1078|transcript|Rv1078|protein_coding|1/1|c.512C>T|p.Thr171Ile|512/723|512/723|171/240||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:769:-69.5275,-6.32163,0
Chromosome	1211369	.	C	A	634.609	.	AB=0;AO=20;DP=20;QA=736;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1086|Rv1086|transcript|Rv1086|protein_coding|1/1|c.775C>A|p.Arg259Ser|775/789|775/789|259/262||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:736:-66.5674,-6.0206,0
Chromosome	1220570	.	T	G	1096.41	.	AB=0;AO=35;DP=35;QA=1253;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|MTS0858-glyA1|RVnc0034-Rv1093|intergenic_region|RVnc0034-Rv1093|||n.1220570T>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1253:-113.063,-10.5361,0
Chromosome	1230778	.	A	G	1055.04	.	AB=0;AO=33;DP=33;QA=1199;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mazF3|Rv1102c|transcript|Rv1102c|protein_coding|1/1|c.194T>C|p.Ile65Thr|194/312|194/312|65/103||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1199:-108.207,-9.93399,0
Chromosome	1231587	.	C	T	614.415	.	AB=0;AO=21;DP=21;QA=706;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|mazE3-Rv1106c|Rv1103c-Rv1106c|intergenic_region|Rv1103c-Rv1106c|||n.1231587C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:706:-63.8433,-6.32163,0
Chromosome	1235446	.	C	T	549.491	.	AB=0;AO=18;DP=18;QA=636;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|xseA|Rv1108c|transcript|Rv1108c|protein_coding|1/1|c.15G>A|p.Ser5Ser|15/1248|15/1248|5/415||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:636:-57.5582,-5.41854,0
Chromosome	1237562	.	G	C	450.284	.	AB=0;AO=15;DP=15;QA=524;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1111c|Rv1111c|transcript|Rv1111c|protein_coding|1/1|c.631C>G|p.Arg211Gly|631/984|631/984|211/327||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:524:-47.4801,-4.51545,0
Chromosome	1244655	.	G	T	737.41	.	AB=0;AO=25;DP=25;QA=846;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|zwf1|Rv1121|transcript|Rv1121|protein_coding|1/1|c.949G>T|p.Ala317Ser|949/1401|949/1401|317/466||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:846:-76.4388,-7.52575,0
Chromosome	1248382	.	G	A	703.554	.	AB=0;AO=22;DP=22;QA=812;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1125|Rv1125|transcript|Rv1125|protein_coding|1/1|c.301G>A|p.Gly101Ser|301/1245|301/1245|101/414||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:812:-73.4031,-6.62266,0
Chromosome	1248936	.	C	G	733.049	.	AB=0;AO=23;DP=23;QA=839;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv1125|Rv1125|transcript|Rv1125|protein_coding|1/1|c.855C>G|p.Pro285Pro|855/1245|855/1245|285/414||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:839:-75.8281,-6.92369,0
Chromosome	1250340	.	G	A	708.49	.	AB=0;AO=23;DP=23;QA=820;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ppdK|Rv1127c|transcript|Rv1127c|protein_coding|1/1|c.1065C>T|p.Ala355Ala|1065/1473|1065/1473|355/490||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:820:-74.1081,-6.92369,0
Chromosome	1250357	.	G	T	727.263	.	AB=0;AO=24;DP=24;QA=843;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ppdK|Rv1127c|transcript|Rv1127c|protein_coding|1/1|c.1048C>A|p.Pro350Thr|1048/1473|1048/1473|350/490||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:843:-76.1714,-7.22472,0
Chromosome	1254562	.	G	A	1117.74	.	AB=0;AO=35;DP=35;QA=1280;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|prpD|Rv1130|transcript|Rv1130|protein_coding|1/1|c.8G>A|p.Gly3Asp|8/1581|8/1581|3/526||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1280:-115.486,-10.5361,0
Chromosome	1256806	.	C	T	907.459	.	AB=0;AO=28;DP=28;QA=1033;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|prpC|Rv1131|transcript|Rv1131|protein_coding|1/1|c.675C>T|p.Asp225Asp|675/1182|675/1182|225/393||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1033:-93.2824,-8.42884,0
Chromosome	1276321	.	TT	GG	698.626	.	AB=0;AO=22;DP=22;QA=804;QR=0;RO=0;TYPE=complex;ANN=GG|missense_variant|MODERATE|Rv1148c|Rv1148c|transcript|Rv1148c|protein_coding|1/1|c.1427_1428delAAinsCC|p.Gln476Pro|1428/1449|1427/1449|476/482||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:804:-72.6806,-6.62266,0
Chromosome	1276360	.	TATTCGC	GATGCGT	575.775	.	AB=0;AO=18;DP=18;QA=663;QR=0;RO=0;TYPE=complex;ANN=GATGCGT|synonymous_variant|LOW|Rv1148c|Rv1148c|transcript|Rv1148c|protein_coding|1/1|c.1383_1389delGCGAATAinsACGCATC|p.464|1389/1449|1383/1449|461/482||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:663:-60.0025,-5.41854,0
Chromosome	1276931	.	T	G	471.056	.	AB=0;AO=15;DP=15;QA=556;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1148c|Rv1148c|transcript|Rv1148c|protein_coding|1/1|c.818A>C|p.Asp273Ala|818/1449|818/1449|273/482||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:556:-50.3768,-4.51545,0
Chromosome	1277869	.	G	GT	632.672	.	AB=0;AO=20;DP=20;QA=731;QR=0;RO=0;TYPE=ins;ANN=GT|intergenic_region|MODIFIER|Rv1148c-Rv1149|Rv1148c-Rv1149|intergenic_region|Rv1148c-Rv1149|||n.1277869_1277870insT||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:731:-66.1141,-6.0206,0
Chromosome	1281771	.	C	T	773.812	.	AB=0;AO=24;DP=24;QA=885;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1155|Rv1155|transcript|Rv1155|protein_coding|1/1|c.343C>T|p.Pro115Ser|343/444|343/444|115/147||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:885:-79.9682,-7.22472,0
Chromosome	1287112	.	C	T	1029.57	.	AB=0;AO=32;DP=32;QA=1178;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|mutT2-narG|Rv1160-Rv1161|intergenic_region|Rv1160-Rv1161|||n.1287112C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1178:-106.319,-9.63296,0
Chromosome	1292464	.	C	T	644.842	.	AB=0;AO=21;DP=21;QA=745;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|narH|Rv1162|transcript|Rv1162|protein_coding|1/1|c.1400C>T|p.Ala467Val|1400/1677|1400/1677|467/558||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:745:-67.3679,-6.32163,0
Chromosome	1302161	.	C	G	365.089	.	AB=0;AO=12;DP=12;QA=425;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|PE12|Rv1172c|transcript|Rv1172c|protein_coding|1/1|c.521G>C|p.Gly174Ala|521/927|521/927|174/308||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:425:-38.5829,-3.61236,0
Chromosome	1310316	.	T	C	493.535	.	AB=0;AO=17;DP=17;QA=577;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1178|Rv1178|transcript|Rv1178|protein_coding|1/1|c.953T>C|p.Val318Ala|953/1089|953/1089|318/362||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:577:-52.2399,-5.11751,0
Chromosome	1312176	.	C	T	474.763	.	AB=0;AO=15;DP=15;QA=551;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1179c|Rv1179c|transcript|Rv1179c|protein_coding|1/1|c.1124G>A|p.Arg375Gln|1124/2820|1124/2820|375/939||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:551:-49.928,-4.51545,0
Chromosome	1313338	.	G	GC	694.442	.	AB=0;AO=22;DP=22;QA=796;QR=0;RO=0;TYPE=ins;ANN=GC|intergenic_region|MODIFIER|Rv1179c-pks3|Rv1179c-Rv1180|intergenic_region|Rv1179c-Rv1180|||n.1313338_1313339insC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:796:-71.9564,-6.62266,0
Chromosome	1340052	.	T	G	429.463	.	AB=0;AO=14;DP=14;QA=502;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|PPE18|Rv1196|transcript|Rv1196|protein_coding|1/1|c.704T>G|p.Leu235Arg|704/1176|704/1176|235/391||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:502:-45.5091,-4.21442,0
Chromosome	1340667	.	A	G	642.362	.	AB=0;AO=20;DP=20;QA=738;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|esxK|Rv1197|transcript|Rv1197|protein_coding|1/1|c.9A>G|p.Ser3Ser|9/297|9/297|3/98||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:738:-66.7474,-6.0206,0
Chromosome	1351172	.	G	A	381.79	.	AB=0;AO=14;DP=14;QA=456;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|fadD6-folP2|Rv1206-Rv1207|intergenic_region|Rv1206-Rv1207|||n.1351172G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:456:-41.3439,-4.21442,0
Chromosome	1358940	.	A	C	880.981	.	AB=0;AO=30;DP=30;QA=1023;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1215c|Rv1215c|transcript|Rv1215c|protein_coding|1/1|c.505T>G|p.Ser169Ala|505/1686|505/1686|169/561||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1023:-92.3609,-9.0309,0
Chromosome	1365410	.	G	A	386.428	.	AB=0;AO=13;DP=13;QA=457;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|rseA|Rv1222|transcript|Rv1222|protein_coding|1/1|c.67G>A|p.Ala23Thr|67/465|67/465|23/154||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:457:-41.4576,-3.91339,0
Chromosome	1365837	.	C	CG	773.138	.	AB=0;AO=26;DP=26;QA=895;QR=0;RO=0;TYPE=ins;ANN=CG|intergenic_region|MODIFIER|rseA-htrA|Rv1222-Rv1223|intergenic_region|Rv1222-Rv1223|||n.1365837_1365838insG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:895:-80.6861,-7.82678,0
Chromosome	1367484	.	G	T	582.87	.	AB=0;AO=18;DP=18;QA=675;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|tatB|Rv1224|transcript|Rv1224|protein_coding|1/1|c.22G>T|p.Gly8Trp|22/396|22/396|8/131||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:675:-61.0844,-5.41854,0
Chromosome	1368947	.	G	A	309.038	.	AB=0;AO=13;DP=13;QA=370;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1226c|Rv1226c|transcript|Rv1226c|protein_coding|1/1|c.1349C>T|p.Ala450Val|1349/1464|1349/1464|450/487||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:370:-33.5705,-3.91339,0
Chromosome	1368961	.	G	A	471.034	.	AB=0;AO=15;DP=15;QA=558;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv1226c|Rv1226c|transcript|Rv1226c|protein_coding|1/1|c.1335C>T|p.Leu445Leu|1335/1464|1335/1464|445/487||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:558:-50.5595,-4.51545,0
Chromosome	1372703	.	C	A	923.262	.	AB=0;AO=29;DP=29;QA=1055;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|mrp|Rv1229c|transcript|Rv1229c|protein_coding|1/1|c.247G>T|p.Val83Leu|247/1173|247/1173|83/390||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1055:-95.2539,-8.72987,0
Chromosome	1390763	.	T	C	1092.54	.	AB=0;AO=34;DP=34;QA=1242;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1248c|Rv1248c|transcript|Rv1248c|protein_coding|1/1|c.2290A>G|p.Met764Val|2290/3696|2290/3696|764/1231||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1242:-112.079,-10.235,0
Chromosome	1393994	.	C	T	918.357	.	AB=0;AO=29;DP=29;QA=1047;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv1249c-Rv1250|Rv1249c-Rv1250|intergenic_region|Rv1249c-Rv1250|||n.1393994C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1047:-94.5309,-8.72987,0
Chromosome	1395010	.	G	A	641.47	.	AB=0;AO=21;DP=21;QA=744;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1250|Rv1250|transcript|Rv1250|protein_coding|1/1|c.832G>A|p.Gly278Arg|832/1740|832/1740|278/579||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:744:-67.2696,-6.32163,0
Chromosome	1396510	.	G	A	669.887	.	AB=0;AO=22;DP=22;QA=774;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1251c|Rv1251c|transcript|Rv1251c|protein_coding|1/1|c.2731C>T|p.His911Tyr|2731/3420|2731/3420|911/1139||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:774:-69.9657,-6.62266,0
Chromosome	1397201	.	G	A	746.24	.	AB=0;AO=24;DP=24;QA=856;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv1251c|Rv1251c|transcript|Rv1251c|protein_coding|1/1|c.2040C>T|p.Asn680Asn|2040/3420|2040/3420|680/1139||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:856:-77.3524,-7.22472,0
Chromosome	1400396	.	G	A	476.572	.	AB=0;AO=16;DP=16;QA=553;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|deaD|Rv1253|transcript|Rv1253|protein_coding|1/1|c.427G>A|p.Val143Met|427/1692|427/1692|143/563||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:553:-50.0863,-4.81648,0
Chromosome	1410062	.	C	G	703.45	.	AB=0;AO=22;DP=22;QA=811;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1262c|Rv1262c|transcript|Rv1262c|protein_coding|1/1|c.311G>C|p.Arg104Pro|311/435|311/435|104/144||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:811:-73.3147,-6.62266,0
Chromosome	1417554	.	C	G	787.531	.	AB=0;AO=27;DP=27;QA=914;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|embR-Rv1268c|Rv1267c-Rv1268c|intergenic_region|Rv1267c-Rv1268c|||n.1417554C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:914:-82.5546,-8.12781,0
Chromosome	1424699	.	C	T	352.773	.	AB=0;AO=13;DP=14;QA=432;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|lprB|Rv1274|transcript|Rv1274|protein_coding|1/1|c.503C>T|p.Pro168Leu|503/558|503/558|168/185||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:13:432:-39.0365,-3.91339,0
Chromosome	1426079	.	C	T	795.406	.	AB=0;AO=27;DP=27;QA=949;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv1276c-Rv1277|Rv1276c-Rv1277|intergenic_region|Rv1276c-Rv1277|||n.1426079C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:949:-85.7066,-8.12781,0
Chromosome	1444202	.	C	G	494.031	.	AB=0;AO=16;DP=16;QA=584;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1290c|Rv1290c|transcript|Rv1290c|protein_coding|1/1|c.846G>C|p.Leu282Phe|846/1566|846/1566|282/521||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:584:-52.8937,-4.81648,0
Chromosome	1458144	.	A	C	562.9	.	AB=0;AO=19;DP=19;QA=650;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1301|Rv1301|transcript|Rv1301|protein_coding|1/1|c.587A>C|p.Gln196Pro|587/654|587/654|196/217||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:650:-58.8134,-5.71957,0
Chromosome	1461915	.	C	G	723.711	.	AB=0;AO=23;DP=23;QA=827;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|atpH|Rv1307|transcript|Rv1307|protein_coding|1/1|c.73C>G|p.Leu25Val|73/1341|73/1341|25/446||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:827:-74.7492,-6.92369,0
Chromosome	1468208	.	A	C	379.07	.	AB=0;AO=13;DP=13;QA=476;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1313c|Rv1313c|transcript|Rv1313c|protein_coding|1/1|c.1298T>G|p.Leu433Arg|1298/1335|1298/1335|433/444||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:476:-43.1781,-3.91339,0
Chromosome	1471539	.	G	A	503.019	.	AB=0;AO=16;DP=16;QA=613;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|murA|Rv1315|transcript|Rv1315|protein_coding|1/1|c.1219G>A|p.Val407Met|1219/1257|1219/1257|407/418||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:613:-55.5086,-4.81648,0
Chromosome	1479085	.	C	T	579.188	.	AB=0;AO=19;DP=19;QA=673;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|alkA|Rv1317c|transcript|Rv1317c|protein_coding|1/1|c.34G>A|p.Val12Ile|34/1491|34/1491|12/496||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:673:-60.8871,-5.71957,0
Chromosome	1483894	.	G	GT	743.453	.	AB=0;AO=24;DP=24;QA=864;QR=0;RO=0;TYPE=ins;ANN=GT|frameshift_variant&stop_gained|HIGH|Rv1320c|Rv1320c|transcript|Rv1320c|protein_coding|1/1|c.323dupA|p.Tyr108fs|323/1704|323/1704|108/567||;LOF=(Rv1320c|Rv1320c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:864:-78.0713,-7.22472,0
Chromosome	1487084	.	C	T	432.403	.	AB=0;AO=17;DP=17;QA=565;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|fadA4-Rv1324|Rv1323-Rv1324|intergenic_region|Rv1323-Rv1324|||n.1487084C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:565:-51.1533,-5.11751,0
Chromosome	1490905	.	G	A	903.163	.	AB=0;AO=29;DP=29;QA=1036;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|glgB|Rv1326c|transcript|Rv1326c|protein_coding|1/1|c.1408C>T|p.Pro470Ser|1408/2196|1408/2196|470/731||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1036:-93.541,-8.72987,0
Chromosome	1490911	.	A	G	922.776	.	AB=0;AO=30;DP=30;QA=1063;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|glgB|Rv1326c|transcript|Rv1326c|protein_coding|1/1|c.1402T>C|p.Ser468Pro|1402/2196|1402/2196|468/731||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1063:-95.9738,-9.0309,0
Chromosome	1492194	.	C	T	330.514	.	AB=0;AO=12;DP=12;QA=401;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|glgB|Rv1326c|transcript|Rv1326c|protein_coding|1/1|c.119G>A|p.Gly40Asp|119/2196|119/2196|40/731||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:401:-36.4086,-3.61236,0
Chromosome	1495326	.	A	G	1493.87	.	AB=0;AO=46;DP=46;QA=1712;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|glgP|Rv1328|transcript|Rv1328|protein_coding|1/1|c.763A>G|p.Lys255Glu|763/2592|763/2592|255/863||	GT:DP:RO:QR:AO:QA:GL	1/1:46:0:0:46:1712:-154.35,-13.8474,0
Chromosome	1496964	.	T	G	538.173	.	AB=0;AO=17;DP=17;QA=632;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|glgP|Rv1328|transcript|Rv1328|protein_coding|1/1|c.2401T>G|p.Ser801Ala|2401/2592|2401/2592|801/863||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:632:-57.2155,-5.11751,0
Chromosome	1505194	.	C	T	421.043	.	AB=0;AO=14;DP=14;QA=494;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|murI|Rv1338|transcript|Rv1338|protein_coding|1/1|c.120C>T|p.Gly40Gly|120/816|120/816|40/271||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:494:-44.792,-4.21442,0
Chromosome	1505973	.	A	G	798.754	.	AB=0;AO=27;DP=27;QA=918;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv1339|Rv1339|transcript|Rv1339|protein_coding|1/1|c.57A>G|p.Arg19Arg|57/822|57/822|19/273||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:918:-82.9152,-8.12781,0
Chromosome	1519431	.	C	T	929.668	.	AB=0;AO=29;DP=29;QA=1068;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1353c|Rv1353c|transcript|Rv1353c|protein_coding|1/1|c.555G>A|p.Val185Val|555/786|555/786|185/261||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1068:-96.4245,-8.72987,0
Chromosome	1523175	.	C	A	358.599	.	AB=0;AO=12;DP=12;QA=424;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|moeY|Rv1355c|transcript|Rv1355c|protein_coding|1/1|c.858G>T|p.Ala286Ala|858/2148|858/2148|286/715||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:424:-38.4902,-3.61236,0
Chromosome	1523791	.	G	A	702.43	.	AB=0;AO=22;DP=22;QA=810;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|moeY|Rv1355c|transcript|Rv1355c|protein_coding|1/1|c.242C>T|p.Pro81Leu|242/2148|242/2148|81/715||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:810:-73.22,-6.62266,0
Chromosome	1533159	.	CCGTG	TCGCC	777.376	.	AB=0;AO=25;DP=25;QA=888;QR=0;RO=0;TYPE=complex;ANN=TCGCC|missense_variant|MODERATE|PPE19|Rv1361c|transcript|Rv1361c|protein_coding|1/1|c.471_475delCACGGinsGGCGA|p.ThrAla158AlaThr|475/1191|471/1191|157/396||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:888:-80.2337,-7.52575,0
Chromosome	1538659	.	T	G	988.502	.	AB=0;AO=31;DP=31;QA=1135;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv1366|Rv1366|transcript|Rv1366|protein_coding|1/1|c.270T>G|p.Arg90Arg|270/822|270/822|90/273||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1135:-102.454,-9.33193,0
Chromosome	1539200	.	G	T	1007.28	.	AB=0;AO=32;DP=32;QA=1145;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained|HIGH|Rv1366|Rv1366|transcript|Rv1366|protein_coding|1/1|c.811G>T|p.Gly271*|811/822|811/822|271/273||,T|synonymous_variant|LOW|Rv1366A|Rv1366A|transcript|Rv1366A|protein_coding|1/1|c.21G>T|p.Gly7Gly|21/261|21/261|7/86||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1145:-103.343,-9.63296,0
Chromosome	1540141	.	C	T	850.337	.	AB=0;AO=26;DP=26;QA=982;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1367c|Rv1367c|transcript|Rv1367c|protein_coding|1/1|c.505G>A|p.Val169Ile|505/1134|505/1134|169/377||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:982:-88.694,-7.82678,0
Chromosome	1544255	.	T	C	741.525	.	AB=0;AO=23;DP=23;QA=850;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1371|Rv1371|transcript|Rv1371|protein_coding|1/1|c.897T>C|p.Arg299Arg|897/1470|897/1470|299/489||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:850:-76.8218,-6.92369,0
Chromosome	1546541	.	A	C	551.646	.	AB=0;AO=18;DP=18;QA=665;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1373|Rv1373|transcript|Rv1373|protein_coding|1/1|c.530A>C|p.Gln177Pro|530/981|530/981|177/326||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:665:-60.1801,-5.41854,0
Chromosome	1546703	.	T	C	516.662	.	AB=0;AO=17;DP=17;QA=597;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1373|Rv1373|transcript|Rv1373|protein_coding|1/1|c.692T>C|p.Leu231Pro|692/981|692/981|231/326||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:597:-54.0552,-5.11751,0
Chromosome	1548087	.	A	G	758.102	.	AB=0;AO=24;DP=24;QA=866;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1375|Rv1375|transcript|Rv1375|protein_coding|1/1|c.256A>G|p.Arg86Gly|256/1320|256/1320|86/439||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:866:-78.2578,-7.22472,0
Chromosome	1550020	.	C	G	423.001	.	AB=0;AO=13;DP=13;QA=493;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1376|Rv1376|transcript|Rv1376|protein_coding|1/1|c.873C>G|p.His291Gln|873/1494|873/1494|291/497||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:493:-44.7169,-3.91339,0
Chromosome	1553633	.	T	C	552.905	.	AB=0;AO=19;DP=19;QA=638;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|pyrB|Rv1380|transcript|Rv1380|protein_coding|1/1|c.402T>C|p.Gly134Gly|402/960|402/960|134/319||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:638:-57.7268,-5.71957,0
Chromosome	1553801	.	G	A	683.841	.	AB=0;AO=23;DP=23;QA=796;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|pyrB|Rv1380|transcript|Rv1380|protein_coding|1/1|c.570G>A|p.Val190Val|570/960|570/960|190/319||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:796:-71.9443,-6.92369,0
Chromosome	1559562	.	A	C	683.892	.	AB=0;AO=21;DP=21;QA=801;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|carB|Rv1384|transcript|Rv1384|protein_coding|1/1|c.2462A>C|p.Glu821Ala|2462/3348|2462/3348|821/1115||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:801:-72.4169,-6.32163,0
Chromosome	1574206	.	C	T	452.299	.	AB=0;AO=15;DP=15;QA=525;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|vapC10|Rv1397c|transcript|Rv1397c|protein_coding|1/1|c.308G>A|p.Gly103Asp|308/402|308/402|103/133||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:525:-47.5689,-4.51545,0
Chromosome	1580680	.	C	T	788.603	.	AB=0;AO=25;DP=25;QA=902;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1404|Rv1404|transcript|Rv1404|protein_coding|1/1|c.90C>T|p.Ala30Ala|90/483|90/483|30/160||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:902:-81.4903,-7.52575,0
Chromosome	1584379	.	C	A	602.113	.	AB=0;AO=21;DP=21;QA=695;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|fmu|Rv1407|transcript|Rv1407|protein_coding|1/1|c.1279C>A|p.Leu427Ile|1279/1374|1279/1374|427/457||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:695:-62.8519,-6.32163,0
Chromosome	1585283	.	C	A	525.733	.	AB=0;AO=17;DP=17;QA=606;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ribG|Rv1409|transcript|Rv1409|protein_coding|1/1|c.90C>A|p.Asn30Lys|90/1020|90/1020|30/339||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:606:-54.8654,-5.11751,0
Chromosome	1585404	.	A	G	614.62	.	AB=0;AO=20;DP=20;QA=711;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ribG|Rv1409|transcript|Rv1409|protein_coding|1/1|c.211A>G|p.Thr71Ala|211/1020|211/1020|71/339||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:711:-64.3089,-6.0206,0
Chromosome	1589383	.	A	G	640.292	.	AB=0;AO=21;DP=21;QA=740;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|ribC-Rv1413|Rv1412-Rv1413|intergenic_region|Rv1412-Rv1413|||n.1589383A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:740:-66.9129,-6.32163,0
Chromosome	1591152	.	C	T	719.777	.	AB=0;AO=23;DP=23;QA=830;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ribA2|Rv1415|transcript|Rv1415|protein_coding|1/1|c.756C>T|p.Asp252Asp|756/1278|756/1278|252/425||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:830:-75.015,-6.92369,0
Chromosome	1600685	.	T	C	542.303	.	AB=0;AO=18;DP=18;QA=628;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1425|Rv1425|transcript|Rv1425|protein_coding|1/1|c.1028T>C|p.Leu343Pro|1028/1380|1028/1380|343/459||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:628:-56.8394,-5.41854,0
Chromosome	1605149	.	C	T	545.598	.	AB=0;AO=17;DP=17;QA=628;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1429|Rv1429|transcript|Rv1429|protein_coding|1/1|c.272C>T|p.Pro91Leu|272/1269|272/1269|91/422||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:628:-56.8519,-5.11751,0
Chromosome	1608276	.	C	A	570.456	.	AB=0;AO=20;DP=20;QA=664;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1431|Rv1431|transcript|Rv1431|protein_coding|1/1|c.194C>A|p.Thr65Asn|194/1770|194/1770|65/589||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:664:-60.062,-6.0206,0
Chromosome	1611283	.	C	T	698.292	.	AB=0;AO=23;DP=23;QA=803;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv1432-Rv1433|Rv1432-Rv1433|intergenic_region|Rv1432-Rv1433|||n.1611283C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:803:-72.571,-6.92369,0
Chromosome	1612278	.	G	GCGTCGA	370.297	.	AB=0;AO=14;DP=14;QA=434;QR=0;RO=0;TYPE=ins;ANN=GCGTCGA|disruptive_inframe_insertion|MODERATE|Rv1434|Rv1434|transcript|Rv1434|protein_coding|1/1|c.26_31dupTCGACG|p.Val9_Asp10dup|32/138|32/138|11/45||INFO_REALIGN_3_PRIME	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:434:-39.3584,-4.21442,0
Chromosome	1617735	.	G	A	375.377	.	AB=0;AO=14;DP=14;QA=466;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv1439c-secG|Rv1439c-Rv1440|intergenic_region|Rv1439c-Rv1440|||n.1617735G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:466:-42.2558,-4.21442,0
Chromosome	1638364	.	T	C	541.166	.	AB=0;AO=17;DP=17;QA=622;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|PE_PGRS28-Rv1453|Rv1452c-Rv1453|intergenic_region|Rv1452c-Rv1453|||n.1638364T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:622:-56.3118,-5.11751,0
Chromosome	1639418	.	G	A	633.448	.	AB=0;AO=20;DP=20;QA=730;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv1453|Rv1453|transcript|Rv1453|protein_coding|1/1|c.1038G>A|p.Leu346Leu|1038/1266|1038/1266|346/421||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:730:-66.0253,-6.0206,0
Chromosome	1639643	.	C	T	689.888	.	AB=0;AO=24;DP=24;QA=812;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1453|Rv1453|transcript|Rv1453|protein_coding|1/1|c.1263C>T|p.Arg421Arg|1263/1266|1263/1266|421/421||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:812:-73.3749,-7.22472,0
Chromosome	1640442	.	T	C	726.386	.	AB=0;AO=24;DP=24;QA=838;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|qor|Rv1454c|transcript|Rv1454c|protein_coding|1/1|c.219A>G|p.Gly73Gly|219/987|219/987|73/328||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:838:-75.7216,-7.22472,0
Chromosome	1643654	.	G	T	455.367	.	AB=0;AO=14;DP=14;QA=532;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1458c|Rv1458c|transcript|Rv1458c|protein_coding|1/1|c.607C>A|p.Leu203Ile|607/942|607/942|203/313||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:532:-48.2245,-4.21442,0
Chromosome	1645334	.	C	T	429.347	.	AB=0;AO=14;DP=14;QA=520;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1459c|Rv1459c|transcript|Rv1459c|protein_coding|1/1|c.805G>A|p.Val269Ile|805/1776|805/1776|269/591||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:520:-47.141,-4.21442,0
Chromosome	1646431	.	G	C	645.477	.	AB=0;AO=21;DP=21;QA=752;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1460|Rv1460|transcript|Rv1460|protein_coding|1/1|c.246G>C|p.Glu82Asp|246/807|246/807|82/268||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:752:-68.0012,-6.32163,0
Chromosome	1659994	.	T	C	740.197	.	AB=0;AO=24;DP=24;QA=854;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|echA12|Rv1472|transcript|Rv1472|protein_coding|1/1|c.232T>C|p.Ser78Pro|232/858|232/858|78/285||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:854:-77.1684,-7.22472,0
Chromosome	1669358	.	C	A	461.0	.	AB=0;AO=15;DP=15;QA=537;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|moxR1|Rv1479|transcript|Rv1479|protein_coding|1/1|c.76C>A|p.His26Asn|76/1134|76/1134|26/377||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:537:-48.6608,-4.51545,0
Chromosome	1677388	.	G	A	500.269	.	AB=0;AO=17;DP=17;QA=579;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv1487-Rv1488|Rv1487-Rv1488|intergenic_region|Rv1487-Rv1488|||n.1677388G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:579:-52.4158,-5.11751,0
Chromosome	1688300	.	C	T	538.233	.	AB=0;AO=17;DP=17;QA=622;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|lipL|Rv1497|transcript|Rv1497|protein_coding|1/1|c.360C>T|p.Phe120Phe|360/1290|360/1290|120/429||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:622:-56.3116,-5.11751,0
Chromosome	1689571	.	C	G	886.66	.	AB=0;AO=27;DP=27;QA=1019;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1498c|Rv1498c|transcript|Rv1498c|protein_coding|1/1|c.350G>C|p.Cys117Ser|350/618|350/618|117/205||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:1019:-92.0232,-8.12781,0
Chromosome	1694547	.	C	A	922.663	.	AB=0;AO=29;DP=29;QA=1061;QR=0;RO=0;TYPE=snp;ANN=A|intragenic_variant|MODIFIER|Rv1503c|Rv1503c|gene_variant|Rv1503c|||n.1694547C>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1061:-95.792,-8.72987,0
Chromosome	1695674	.	A	G	1157.99	.	AB=0;AO=35;DP=35;QA=1317;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv1505c|Rv1505c|transcript|Rv1505c|protein_coding|1/1|c.273T>C|p.Tyr91Tyr|273/666|273/666|91/221||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1317:-118.824,-10.5361,0
Chromosome	1699849	.	A	G	631.866	.	AB=0;AO=21;DP=21;QA=728;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1508c|Rv1508c|transcript|Rv1508c|protein_coding|1/1|c.46T>C|p.Ser16Pro|46/1800|46/1800|16/599||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:728:-65.8273,-6.32163,0
Chromosome	1704554	.	C	T	548.48	.	AB=0;AO=18;DP=18;QA=637;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|epiA|Rv1512|transcript|Rv1512|protein_coding|1/1|c.462C>T|p.Ile154Ile|462/969|462/969|154/322||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:637:-57.6454,-5.41854,0
Chromosome	1706746	.	A	C	588.298	.	AB=0;AO=19;DP=19;QA=688;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1515c|Rv1515c|transcript|Rv1515c|protein_coding|1/1|c.781T>G|p.Phe261Val|781/897|781/897|261/298||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:688:-62.2431,-5.71957,0
Chromosome	1711645	.	T	C	677.227	.	AB=0;AO=22;DP=22;QA=789;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1520|Rv1520|transcript|Rv1520|protein_coding|1/1|c.618T>C|p.Gly206Gly|618/1041|618/1041|206/346||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:789:-71.3244,-6.62266,0
Chromosome	1711692	.	G	A	809.307	.	AB=0;AO=26;DP=26;QA=929;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1520|Rv1520|transcript|Rv1520|protein_coding|1/1|c.665G>A|p.Arg222Gln|665/1041|665/1041|222/346||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:929:-83.9143,-7.82678,0
Chromosome	1716472	.	G	A	482.986	.	AB=0;AO=17;DP=17;QA=562;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|mmpL12|Rv1522c|transcript|Rv1522c|protein_coding|1/1|c.1141C>T|p.Pro381Ser|1141/3441|1141/3441|381/1146||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:562:-50.8839,-5.11751,0
Chromosome	1724722	.	T	C	1024.4	.	AB=0;AO=32;DP=32;QA=1171;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|pks5|Rv1527c|transcript|Rv1527c|protein_coding|1/1|c.3688A>G|p.Thr1230Ala|3688/6327|3688/6327|1230/2108||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1171:-105.692,-9.63296,0
Chromosome	1726816	.	T	G	601.198	.	AB=0;AO=20;DP=20;QA=699;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|pks5|Rv1527c|transcript|Rv1527c|protein_coding|1/1|c.1594A>C|p.Thr532Pro|1594/6327|1594/6327|532/2108||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:699:-63.2263,-6.0206,0
Chromosome	1728622	.	C	G	694.869	.	AB=0;AO=23;DP=23;QA=796;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|pks5-papA4|Rv1527c-Rv1528c|intergenic_region|Rv1527c-Rv1528c|||n.1728622C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:796:-71.9375,-6.92369,0
Chromosome	1760923	.	C	T	386.565	.	AB=0;AO=13;DP=13;QA=472;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|frdD|Rv1555|transcript|Rv1555|protein_coding|1/1|c.372C>T|p.Thr124Thr|372/378|372/378|124/125||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:472:-42.8137,-3.91339,0
Chromosome	1761789	.	C	G	684.06	.	AB=0;AO=21;DP=21;QA=784;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mmpL6|Rv1557|transcript|Rv1557|protein_coding|1/1|c.46C>G|p.Leu16Val|46/1194|46/1194|16/397||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:784:-70.887,-6.32163,0
Chromosome	1769469	.	C	A	834.759	.	AB=0;AO=26;DP=26;QA=963;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|treX|Rv1564c|transcript|Rv1564c|protein_coding|1/1|c.2133G>T|p.Ala711Ala|2133/2166|2133/2166|711/721||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:963:-86.9818,-7.82678,0
Chromosome	1772742	.	G	A	570.211	.	AB=0;AO=19;DP=19;QA=683;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1565c|Rv1565c|transcript|Rv1565c|protein_coding|1/1|c.1088C>T|p.Ala363Val|1088/2190|1088/2190|363/729||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:683:-61.7944,-5.71957,0
Chromosome	1797577	.	G	A	536.356	.	AB=0;AO=17;DP=17;QA=630;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|nadC|Rv1596|transcript|Rv1596|protein_coding|1/1|c.190G>A|p.Asp64Asn|190/858|190/858|64/285||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:630:-57.0338,-5.11751,0
Chromosome	1826054	.	C	T	837.583	.	AB=0;AO=26;DP=26;QA=964;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1624c|Rv1624c|transcript|Rv1624c|protein_coding|1/1|c.532G>A|p.Ala178Thr|532/588|532/588|178/195||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:964:-87.0752,-7.82678,0
Chromosome	1833684	.	G	C	757.053	.	AB=0;AO=25;DP=25;QA=876;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|rpsA|Rv1630|transcript|Rv1630|protein_coding|1/1|c.143G>C|p.Arg48Pro|143/1446|143/1446|48/481||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:876:-79.1476,-7.52575,0
Chromosome	1834130	.	G	A	1435.74	.	AB=0;AO=44;DP=44;QA=1626;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|rpsA|Rv1630|transcript|Rv1630|protein_coding|1/1|c.589G>A|p.Glu197Lys|589/1446|589/1446|197/481||	GT:DP:RO:QR:AO:QA:GL	1/1:44:0:0:44:1626:-146.612,-13.2453,0
Chromosome	1839260	.	G	T	459.572	.	AB=0;AO=15;DP=15;QA=538;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1634|Rv1634|transcript|Rv1634|protein_coding|1/1|c.93G>T|p.Leu31Leu|93/1416|93/1416|31/471||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:538:-48.7513,-4.51545,0
Chromosome	1839759	.	C	G	871.137	.	AB=0;AO=28;DP=28;QA=994;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1634|Rv1634|transcript|Rv1634|protein_coding|1/1|c.592C>G|p.Arg198Gly|592/1416|592/1416|198/471||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:994:-89.7703,-8.42884,0
Chromosome	1849119	.	G	C	483.535	.	AB=0;AO=16;DP=16;QA=563;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|lysX|Rv1640c|transcript|Rv1640c|protein_coding|1/1|c.2917C>G|p.Arg973Gly|2917/3519|2917/3519|973/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:563:-50.9946,-4.81648,0
Chromosome	1849609	.	C	T	680.286	.	AB=0;AO=22;DP=22;QA=801;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|lysX|Rv1640c|transcript|Rv1640c|protein_coding|1/1|c.2427G>A|p.Arg809Arg|2427/3519|2427/3519|809/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:801:-72.411,-6.62266,0
Chromosome	1859559	.	A	C	650.462	.	AB=0;AO=21;DP=21;QA=754;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|pheS|Rv1649|transcript|Rv1649|protein_coding|1/1|c.827A>C|p.Asp276Ala|827/1026|827/1026|276/341||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:754:-68.1817,-6.32163,0
Chromosome	1868578	.	C	T	523.929	.	AB=0;AO=17;DP=17;QA=630;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|argB|Rv1654|transcript|Rv1654|protein_coding|1/1|c.737C>T|p.Ser246Leu|737/885|737/885|246/294||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:630:-57.0288,-5.11751,0
Chromosome	1872906	.	G	T	427.46	.	AB=0;AO=15;DP=15;QA=509;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|argH|Rv1659|transcript|Rv1659|protein_coding|1/1|c.268G>T|p.Ala90Ser|268/1413|268/1413|90/470||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:509:-46.1264,-4.51545,0
Chromosome	1872959	.	G	A	343.481	.	AB=0;AO=11;DP=11;QA=401;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|argH|Rv1659|transcript|Rv1659|protein_coding|1/1|c.321G>A|p.Arg107Arg|321/1413|321/1413|107/470||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:401:-36.4343,-3.31133,0
Chromosome	1875207	.	C	T	380.365	.	AB=0;AO=12;DP=12;QA=451;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|pks10|Rv1660|transcript|Rv1660|protein_coding|1/1|c.1048C>T|p.Leu350Leu|1048/1062|1048/1062|350/353||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:451:-40.9378,-3.61236,0
Chromosome	1884697	.	G	A	726.783	.	AB=0;AO=24;DP=24;QA=844;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|pks8|Rv1662|transcript|Rv1662|protein_coding|1/1|c.2994G>A|p.Gly998Gly|2994/4809|2994/4809|998/1602||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:844:-76.2648,-7.22472,0
Chromosome	1888128	.	A	G	668.505	.	AB=0;AO=21;DP=21;QA=774;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|pks9|Rv1664|transcript|Rv1664|protein_coding|1/1|c.103A>G|p.Thr35Ala|103/3054|103/3054|35/1017||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:774:-69.9861,-6.32163,0
Chromosome	1889073	.	C	G	510.836	.	AB=0;AO=16;DP=16;QA=592;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|pks9|Rv1664|transcript|Rv1664|protein_coding|1/1|c.1048C>G|p.Pro350Ala|1048/3054|1048/3054|350/1017||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:592:-53.6164,-4.81648,0
Chromosome	1894300	.	G	GGTCTTGCCGC	493.249	.	AB=0;AO=16;DP=16;QA=576;QR=0;RO=0;TYPE=ins;ANN=GGTCTTGCCGC|intragenic_variant|MODIFIER|Rv1667c|Rv1667c|gene_variant|Rv1667c|||n.1894300_1894301insGTCTTGCCGC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:576:-52.1721,-4.81648,0
Chromosome	1896387	.	T	C	1045.24	.	AB=0;AO=33;DP=33;QA=1191;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1670|Rv1670|transcript|Rv1670|protein_coding|1/1|c.268T>C|p.Trp90Arg|268/348|268/348|90/115||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1191:-107.484,-9.93399,0
Chromosome	1900800	.	G	A	759.231	.	AB=0;AO=25;DP=25;QA=871;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|cmr|Rv1675c|transcript|Rv1675c|protein_coding|1/1|c.176C>T|p.Ala59Val|176/735|176/735|59/244||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:871:-78.6878,-7.52575,0
Chromosome	1906336	.	G	A	848.024	.	AB=0;AO=27;DP=27;QA=986;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|moeX-Rv1682|Rv1681-Rv1682|intergenic_region|Rv1681-Rv1682|||n.1906336G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:986:-89.0533,-8.12781,0
Chromosome	1920120	.	T	G	731.299	.	AB=0;AO=24;DP=24;QA=841;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|recN|Rv1696|transcript|Rv1696|protein_coding|1/1|c.438T>G|p.Pro146Pro|438/1764|438/1764|146/587||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:841:-75.9978,-7.22472,0
Chromosome	1924959	.	C	T	883.48	.	AB=0;AO=29;DP=29;QA=1007;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|pyrG|Rv1699|transcript|Rv1699|protein_coding|1/1|c.1131C>T|p.Gly377Gly|1131/1761|1131/1761|377/586||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1007:-90.9267,-8.72987,0
Chromosome	1931470	.	A	G	321.458	.	AB=0;AO=10;DP=10;QA=378;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|cycA-PPE22|Rv1704c-Rv1705c|intergenic_region|Rv1704c-Rv1705c|||n.1931470A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:378:-34.3739,-3.0103,0
Chromosome	1931564	.	G	A	302.094	.	AB=0;AO=11;DP=11;QA=357;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|PPE22|Rv1705c|transcript|Rv1705c|protein_coding|1/1|c.1091C>T|p.Thr364Met|1091/1158|1091/1158|364/385||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:357:-32.4418,-3.31133,0
Chromosome	1931718	.	C	G	446.243	.	AB=0;AO=16;DP=16;QA=530;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|PPE22|Rv1705c|transcript|Rv1705c|protein_coding|1/1|c.937G>C|p.Val313Leu|937/1158|937/1158|313/385||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:530:-48.0067,-4.81648,0
Chromosome	1935695	.	G	T	817.618	.	AB=0;AO=26;DP=26;QA=936;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1707|Rv1707|transcript|Rv1707|protein_coding|1/1|c.814G>T|p.Ala272Ser|814/1461|814/1461|272/486||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:936:-84.5471,-7.82678,0
Chromosome	1936525	.	A	G	802.397	.	AB=0;AO=25;DP=25;QA=918;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1708|Rv1708|transcript|Rv1708|protein_coding|1/1|c.166A>G|p.Thr56Ala|166/957|166/957|56/318||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:918:-82.9375,-7.52575,0
Chromosome	1939763	.	A	G	654.655	.	AB=0;AO=21;DP=21;QA=764;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|cmk|Rv1712|transcript|Rv1712|protein_coding|1/1|c.165A>G|p.Pro55Pro|165/693|165/693|55/230||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:764:-69.083,-6.32163,0
Chromosome	1940258	.	G	A	910.681	.	AB=0;AO=31;DP=31;QA=1047;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|cmk|Rv1712|transcript|Rv1712|protein_coding|1/1|c.660G>A|p.Glu220Glu|660/693|660/693|220/230||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1047:-94.5155,-9.33193,0
Chromosome	1951626	.	GC	G	449.677	.	AB=0;AO=17;DP=18;QA=527;QR=0;RO=0;TYPE=del;ANN=G|frameshift_variant|HIGH|Rv1725c|Rv1725c|transcript|Rv1725c|protein_coding|1/1|c.125delG|p.Gly42fs|125/711|125/711|42/236||;LOF=(Rv1725c|Rv1725c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:17:527:-47.2598,-5.11751,0
Chromosome	1952160	.	C	T	300.187	.	AB=0;AO=10;DP=10;QA=351;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1726|Rv1726|transcript|Rv1726|protein_coding|1/1|c.309C>T|p.Thr103Thr|309/1386|309/1386|103/461||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:351:-31.9246,-3.0103,0
Chromosome	1956523	.	AG	CA	1051.27	.	AB=0;AO=33;DP=33;QA=1200;QR=0;RO=0;TYPE=complex;ANN=CA|missense_variant|MODERATE|Rv1730c|Rv1730c|transcript|Rv1730c|protein_coding|1/1|c.722_723delCTinsTG|p.Thr241Met|723/1554|722/1554|241/517||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1200:-108.296,-9.93399,0
Chromosome	1960391	.	G	A	935.8	.	AB=0;AO=29;DP=29;QA=1067;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1733c|Rv1733c|transcript|Rv1733c|protein_coding|1/1|c.97C>T|p.Pro33Ser|97/633|97/633|33/210||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1067:-96.3332,-8.72987,0
Chromosome	1962071	.	AGG	A	679.882	.	AB=0;AO=24;DP=24;QA=788;QR=0;RO=0;TYPE=del;ANN=A|frameshift_variant|HIGH|Rv1735a|Rv1735a|transcript|Rv1735a|protein_coding|1/1|c.57_58delCC|p.Leu20fs|58/243|57/243|19/80||;LOF=(Rv1735a|Rv1735a|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:788:-71.2107,-7.22472,0
Chromosome	1963957	.	C	T	880.274	.	AB=0;AO=29;DP=29;QA=1008;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|narX|Rv1736c|transcript|Rv1736c|protein_coding|1/1|c.230G>A|p.Gly77Asp|230/1959|230/1959|77/652||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1008:-91.0147,-8.72987,0
Chromosome	1964719	.	C	T	1150.94	.	AB=0;AO=35;DP=35;QA=1307;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|narK2|Rv1737c|transcript|Rv1737c|protein_coding|1/1|c.652G>A|p.Val218Met|652/1188|652/1188|218/395||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1307:-117.925,-10.5361,0
Chromosome	1971725	.	C	G	360.402	.	AB=0;AO=12;DP=12;QA=431;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|idi|Rv1745c|transcript|Rv1745c|protein_coding|1/1|c.267G>C|p.Arg89Arg|267/612|267/612|89/203||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:431:-39.1264,-3.61236,0
Chromosome	1989054	.	ATCG	TTCA	421.025	.	AB=0;AO=14;DP=14;QA=494;QR=0;RO=0;TYPE=complex;ANN=TTCA|missense_variant|MODERATE|cut1|Rv1758|transcript|Rv1758|protein_coding|1/1|c.13_16delATCGinsTTCA|p.IleGly5PheArg|13/525|13/525|5/174||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:494:-44.7902,-4.21442,0
Chromosome	2007502	.	G	A	460.726	.	AB=0;AO=15;DP=15;QA=543;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1773c|Rv1773c|transcript|Rv1773c|protein_coding|1/1|c.265C>T|p.His89Tyr|265/747|265/747|89/248||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:543:-49.1977,-4.51545,0
Chromosome	2008870	.	C	G	695.911	.	AB=0;AO=22;DP=22;QA=801;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1774|Rv1774|transcript|Rv1774|protein_coding|1/1|c.1039C>G|p.Leu347Val|1039/1341|1039/1341|347/446||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:801:-72.409,-6.62266,0
Chromosome	2010614	.	A	G	640.725	.	AB=0;AO=21;DP=21;QA=748;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv1776c-cyp144|Rv1776c-Rv1777|intergenic_region|Rv1776c-Rv1777|||n.2010614A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:748:-67.634,-6.32163,0
Chromosome	2014185	.	C	T	639.921	.	AB=0;AO=21;DP=21;QA=736;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1779c|Rv1779c|transcript|Rv1779c|protein_coding|1/1|c.295G>A|p.Ala99Thr|295/1794|295/1794|99/597||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:736:-66.5536,-6.32163,0
Chromosome	2017291	.	C	T	1058.35	.	AB=0;AO=34;DP=34;QA=1216;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|malQ|Rv1781c|transcript|Rv1781c|protein_coding|1/1|c.186G>A|p.Arg62Arg|186/2175|186/2175|62/724||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1216:-109.736,-10.235,0
Chromosome	2019236	.	G	T	486.232	.	AB=0;AO=16;DP=16;QA=566;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|eccB5|Rv1782|transcript|Rv1782|protein_coding|1/1|c.1497G>T|p.Pro499Pro|1497/1521|1497/1521|499/506||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:566:-51.2643,-4.81648,0
Chromosome	2020144	.	G	A	315.502	.	AB=0;AO=10;DP=10;QA=375;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|eccC5|Rv1783|transcript|Rv1783|protein_coding|1/1|c.888G>A|p.Glu296Glu|888/4176|888/4176|296/1391||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:375:-34.1005,-3.0103,0
Chromosome	2026148	.	C	T	547.418	.	AB=0;AO=17;DP=17;QA=630;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE25|Rv1787|transcript|Rv1787|protein_coding|1/1|c.848C>T|p.Ala283Val|848/1098|848/1098|283/365||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:630:-57.0339,-5.11751,0
Chromosome	2030942	.	G	A	396.382	.	AB=0;AO=13;DP=13;QA=465;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|esxN|Rv1793|transcript|Rv1793|protein_coding|1/1|c.249G>A|p.Ala83Ala|249/285|249/285|83/94||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:465:-42.18,-3.91339,0
Chromosome	2037698	.	G	A	1226.96	.	AB=0;AO=38;DP=38;QA=1391;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|eccA5|Rv1798|transcript|Rv1798|protein_coding|1/1|c.999G>A|p.Thr333Thr|999/1833|999/1833|333/610||	GT:DP:RO:QR:AO:QA:GL	1/1:38:0:0:38:1391:-125.48,-11.4391,0
Chromosome	2039884	.	G	T	580.145	.	AB=0;AO=19;DP=19;QA=676;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE28|Rv1800|transcript|Rv1800|protein_coding|1/1|c.432G>T|p.Trp144Cys|432/1968|432/1968|144/655||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:676:-61.159,-5.71957,0
Chromosome	2039901	.	C	T	552.145	.	AB=0;AO=17;DP=17;QA=644;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE28|Rv1800|transcript|Rv1800|protein_coding|1/1|c.449C>T|p.Ala150Val|449/1968|449/1968|150/655||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:644:-58.2971,-5.11751,0
Chromosome	2050061	.	G	A	700.555	.	AB=0;AO=22;DP=22;QA=802;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|PPE32|Rv1808|transcript|Rv1808|protein_coding|1/1|c.141G>A|p.Ser47Ser|141/1230|141/1230|47/409||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:802:-72.4915,-6.62266,0
Chromosome	2050822	.	C	G	803.329	.	AB=0;AO=26;DP=26;QA=931;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|PPE32|Rv1808|transcript|Rv1808|protein_coding|1/1|c.902C>G|p.Ala301Gly|902/1230|902/1230|301/409||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:931:-84.0984,-7.82678,0
Chromosome	2052687	.	C	G	803.869	.	AB=0;AO=26;DP=26;QA=926;QR=0;RO=0;TYPE=snp;ANN=G|stop_gained&splice_region_variant|HIGH|PPE33|Rv1809|transcript|Rv1809|protein_coding|1/1|c.1406C>G|p.Ser469*|1406/1407|1406/1407|469/468||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:926:-83.6394,-7.82678,0
Chromosome	2054805	.	G	A	473.669	.	AB=0;AO=16;DP=16;QA=558;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv1812c|Rv1812c|transcript|Rv1812c|protein_coding|1/1|c.555C>T|p.Pro185Pro|555/1203|555/1203|185/400||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:558:-50.5431,-4.81648,0
Chromosome	2056450	.	T	C	924.605	.	AB=0;AO=29;DP=29;QA=1052;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv1813c-erg3|Rv1813c-Rv1814|intergenic_region|Rv1813c-Rv1814|||n.2056450T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1052:-94.9812,-8.72987,0
Chromosome	2057141	.	G	A	747.125	.	AB=0;AO=24;DP=24;QA=857;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|erg3|Rv1814|transcript|Rv1814|protein_coding|1/1|c.621G>A|p.Pro207Pro|621/903|621/903|207/300||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:857:-77.4409,-7.22472,0
Chromosome	2062922	.	C	T	395.534	.	AB=0;AO=13;DP=13;QA=464;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|bacA|Rv1819c|transcript|Rv1819c|protein_coding|1/1|c.1807G>A|p.Val603Ile|1807/1920|1807/1920|603/639||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:464:-42.0951,-3.91339,0
Chromosome	2065383	.	C	T	576.377	.	AB=0;AO=18;DP=18;QA=670;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ilvG|Rv1820|transcript|Rv1820|protein_coding|1/1|c.585C>T|p.Ala195Ala|585/1644|585/1644|195/547||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:670:-60.6325,-5.41854,0
Chromosome	2072190	.	C	A	993.973	.	AB=0;AO=32;DP=32;QA=1135;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|gcvH|Rv1826|transcript|Rv1826|protein_coding|1/1|c.239C>A|p.Ala80Glu|239/405|239/405|80/134||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1135:-102.437,-9.63296,0
Chromosome	2077218	.	G	A	805.08	.	AB=0;AO=27;DP=27;QA=930;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|gcvB|Rv1832|transcript|Rv1832|protein_coding|1/1|c.1342G>A|p.Ala448Thr|1342/2826|1342/2826|448/941||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:930:-83.9921,-8.12781,0
Chromosome	2081449	.	T	TA	403.943	.	AB=0;AO=15;DP=15;QA=474;QR=0;RO=0;TYPE=ins;ANN=TA|frameshift_variant|HIGH|Rv1835c|Rv1835c|transcript|Rv1835c|protein_coding|1/1|c.1138_1139insT|p.His380fs|1138/1887|1138/1887|380/628||;LOF=(Rv1835c|Rv1835c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:474:-42.9551,-4.51545,0
Chromosome	2087935	.	A	G	378.699	.	AB=0;AO=12;DP=12;QA=443;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|vapB13-PE_PGRS34|Rv1839c-Rv1840c|intergenic_region|Rv1839c-Rv1840c|||n.2087935A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:443:-40.215,-3.61236,0
Chromosome	2090921	.	C	T	703.0	.	AB=0;AO=23;DP=23;QA=819;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1842c|Rv1842c|transcript|Rv1842c|protein_coding|1/1|c.1165G>A|p.Gly389Ser|1165/1368|1165/1368|389/455||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:819:-74.0236,-6.92369,0
Chromosome	2093715	.	C	T	694.755	.	AB=0;AO=22;DP=22;QA=798;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|guaB1-gnd1|Rv1843c-Rv1844c|intergenic_region|Rv1843c-Rv1844c|||n.2093715C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:798:-72.1393,-6.62266,0
Chromosome	2094911	.	ACAGCGT	A	675.375	.	AB=0;AO=22;DP=22;QA=780;QR=0;RO=0;TYPE=del;ANN=A|disruptive_inframe_deletion|MODERATE|gnd1|Rv1844c|transcript|Rv1844c|protein_coding|1/1|c.272_277delACGCTG|p.Asp91_Ala92del|277/1458|272/1458|91/485||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:780:-70.5145,-6.62266,0
Chromosome	2097144	.	C	G	737.979	.	AB=0;AO=24;DP=24;QA=850;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1847|Rv1847|transcript|Rv1847|protein_coding|1/1|c.268C>G|p.Leu90Val|268/423|268/423|90/140||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:850:-76.8071,-7.22472,0
Chromosome	2108890	.	C	A	673.86	.	AB=0;AO=22;DP=22;QA=789;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|apa-Rv1861|Rv1860-Rv1861|intergenic_region|Rv1860-Rv1861|||n.2108890C>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:789:-71.3261,-6.62266,0
Chromosome	2109523	.	C	CG	700.405	.	AB=0;AO=23;DP=24;QA=815;QR=0;RO=0;TYPE=ins;ANN=CG|intergenic_region|MODIFIER|Rv1861-adhA|Rv1861-Rv1862|intergenic_region|Rv1861-Rv1862|||n.2109523_2109524insG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:23:815:-73.2965,-6.92369,0
Chromosome	2110365	.	C	A	438.403	.	AB=0;AO=14;DP=14;QA=512;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|adhA|Rv1862|transcript|Rv1862|protein_coding|1/1|c.822C>A|p.Thr274Thr|822/1041|822/1041|274/346||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:512:-46.412,-4.21442,0
Chromosome	2115210	.	A	C	477.507	.	AB=0;AO=16;DP=16;QA=554;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1866|Rv1866|transcript|Rv1866|protein_coding|1/1|c.2071A>C|p.Asn691His|2071/2337|2071/2337|691/778||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:554:-50.1797,-4.81648,0
Chromosome	2120796	.	A	T	650.003	.	AB=0;AO=21;DP=21;QA=765;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained&splice_region_variant|HIGH|Rv1870c|Rv1870c|transcript|Rv1870c|protein_coding|1/1|c.635T>A|p.Leu212*|635/636|635/636|212/211||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:765:-69.1724,-6.32163,0
Chromosome	2122625	.	G	A	355.914	.	AB=0;AO=12;DP=12;QA=424;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lldD2|Rv1872c|transcript|Rv1872c|protein_coding|1/1|c.527C>T|p.Ala176Val|527/1245|527/1245|176/414||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:424:-38.4927,-3.61236,0
Chromosome	2122976	.	G	C	679.761	.	AB=0;AO=22;DP=22;QA=778;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|lldD2|Rv1872c|transcript|Rv1872c|protein_coding|1/1|c.176C>G|p.Ala59Gly|176/1245|176/1245|59/414||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:778:-70.3365,-6.62266,0
Chromosome	2128372	.	G	A	1120.52	.	AB=0;AO=35;DP=35;QA=1296;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|glnA3|Rv1878|transcript|Rv1878|protein_coding|1/1|c.351G>A|p.Thr117Thr|351/1353|351/1353|117/450||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1296:-116.934,-10.5361,0
Chromosome	2129281	.	A	C	1142.4	.	AB=0;AO=36;DP=36;QA=1296;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|glnA3|Rv1878|transcript|Rv1878|protein_coding|1/1|c.1260A>C|p.Ala420Ala|1260/1353|1260/1353|420/450||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1296:-116.925,-10.8371,0
Chromosome	2130529	.	G	A	621.179	.	AB=0;AO=20;DP=20;QA=722;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv1879-cyp140|Rv1879-Rv1880c|intergenic_region|Rv1879-Rv1880c|||n.2130529G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:722:-65.3006,-6.0206,0
Chromosome	2132152	.	T	C	1003.33	.	AB=0;AO=33;DP=33;QA=1145;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|lppE|Rv1881c|transcript|Rv1881c|protein_coding|1/1|c.178A>G|p.Ile60Val|178/423|178/423|60/140||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1145:-103.345,-9.93399,0
Chromosome	2134325	.	C	T	816.526	.	AB=0;AO=25;DP=25;QA=936;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|*MtCM|Rv1885c|transcript|Rv1885c|protein_coding|1/1|c.548G>A|p.Arg183Gln|548/600|548/600|183/199||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:936:-84.5545,-7.52575,0
Chromosome	2137521	.	A	ACTCCGATCAC	538.468	.	AB=0;AO=20;DP=20;QA=623;QR=0;RO=0;TYPE=ins;ANN=ACTCCGATCAC|intragenic_variant|MODIFIER|Rv1887a|Rv1887a|gene_variant|Rv1887a|||n.2137521_2137522insCTCCGATCAC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:623:-56.3579,-6.0206,0
Chromosome	2145878	.	G	A	477.037	.	AB=0;AO=15;DP=15;QA=561;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lppD|Rv1899c|transcript|Rv1899c|protein_coding|1/1|c.368C>T|p.Pro123Leu|368/1032|368/1032|123/343||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:561:-50.8288,-4.51545,0
Chromosome	2151678	.	T	G	567.333	.	AB=0;AO=19;DP=19;QA=653;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|aao|Rv1905c|transcript|Rv1905c|protein_coding|1/1|c.718A>C|p.Thr240Pro|718/963|718/963|240/320||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:653:-59.0824,-5.71957,0
Chromosome	2152952	.	A	C	769.946	.	AB=0;AO=24;DP=24;QA=891;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv1906c-Rv1907c|Rv1906c-Rv1907c|intergenic_region|Rv1906c-Rv1907c|||n.2152952A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:891:-80.5036,-7.22472,0
Chromosome	2154724	.	A	C	520.057	.	AB=0;AO=17;DP=17;QA=603;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|katG|Rv1908c|transcript|Rv1908c|protein_coding|1/1|c.1388T>G|p.Leu463Arg|1388/2223|1388/2223|463/740||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:603:-54.591,-5.11751,0
Chromosome	2155168	.	C	G	451.514	.	AB=0;AO=15;DP=15;QA=534;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|katG|Rv1908c|transcript|Rv1908c|protein_coding|1/1|c.944G>C|p.Ser315Thr|944/2223|944/2223|315/740||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:534:-48.3856,-4.51545,0
Chromosome	2156868	.	T	G	945.428	.	AB=0;AO=30;DP=30;QA=1076;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv1910c|Rv1910c|transcript|Rv1910c|protein_coding|1/1|c.432A>C|p.Gly144Gly|432/594|432/594|144/197||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1076:-97.1476,-9.0309,0
Chromosome	2157856	.	G	A	349.094	.	AB=0;AO=13;DP=13;QA=420;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|lppC|Rv1911c|transcript|Rv1911c|protein_coding|1/1|c.132C>T|p.Val44Val|132/606|132/606|44/201||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:420:-38.1044,-3.91339,0
Chromosome	2158109	.	C	T	962.365	.	AB=0;AO=30;DP=30;QA=1098;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|fadB5|Rv1912c|transcript|Rv1912c|protein_coding|1/1|c.983G>A|p.Gly328Asp|983/1005|983/1005|328/334||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1098:-99.1232,-9.0309,0
Chromosome	2158582	.	G	A	718.93	.	AB=0;AO=25;DP=25;QA=824;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|fadB5|Rv1912c|transcript|Rv1912c|protein_coding|1/1|c.510C>T|p.Gly170Gly|510/1005|510/1005|170/334||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:824:-74.4561,-7.52575,0
Chromosome	2161343	.	G	GT	358.295	.	AB=0;AO=12;DP=12;QA=425;QR=0;RO=0;TYPE=ins;ANN=GT|frameshift_variant|HIGH|aceAa|Rv1915|transcript|Rv1915|protein_coding|1/1|c.885dupT|p.Thr296fs|886/1104|886/1104|296/367||INFO_REALIGN_3_PRIME;LOF=(aceAa|Rv1915|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:425:-38.5828,-3.61236,0
Chromosome	2162803	.	T	C	928.336	.	AB=0;AO=29;DP=29;QA=1058;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|aceAb-PPE34|Rv1916-Rv1917c|intergenic_region|Rv1916-Rv1917c|||n.2162803T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1058:-95.5288,-8.72987,0
Chromosome	2163375	.	T	C	411.354	.	AB=0;AO=15;DP=16;QA=507;QR=27;RO=1;TYPE=snp;ANN=C|missense_variant|MODERATE|PPE34|Rv1917c|transcript|Rv1917c|protein_coding|1/1|c.3937A>G|p.Asn1313Asp|3937/4380|3937/4380|1313/1459||	GT:DP:RO:QR:AO:QA:GL	1/1:16:1:27:15:507:-43.2448,-2.1167,0
Chromosome	2167926	.	G	A	517.493	.	AB=0;AO=17;DP=17;QA=598;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|PPE35|Rv1918c|transcript|Rv1918c|protein_coding|1/1|c.2687C>T|p.Ser896Leu|2687/2964|2687/2964|896/987||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:598:-54.1383,-5.11751,0
Chromosome	2177073	.	C	T	507.359	.	AB=0;AO=17;DP=17;QA=590;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv1924c-fadD31|Rv1924c-Rv1925|intergenic_region|Rv1924c-Rv1925|||n.2177073C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:590:-53.4181,-5.11751,0
Chromosome	2180796	.	CCGCCTTGGCCTTGTTTGACCAT	C	420.501	.	AB=0;AO=16;DP=16;QA=491;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv1928c|Rv1928c|transcript|Rv1928c|protein_coding|1/1|c.400_421delATGGTCAAACAAGGCCAAGGCG|p.Met134fs|421/768|400/768|134/255||;LOF=(Rv1928c|Rv1928c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:491:-44.4792,-4.81648,0
Chromosome	2187274	.	C	A	808.763	.	AB=0;AO=26;DP=26;QA=927;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|echA13-Rv1936|Rv1935c-Rv1936|intergenic_region|Rv1935c-Rv1936|||n.2187274C>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:927:-83.7264,-7.82678,0
Chromosome	2197176	.	A	G	368.126	.	AB=0;AO=12;DP=12;QA=441;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv1945|Rv1945|transcript|Rv1945|protein_coding|1/1|c.1188A>G|p.Thr396Thr|1188/1365|1188/1365|396/454||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:441:-40.0327,-3.61236,0
Chromosome	2199052	.	G	C	590.968	.	AB=0;AO=18;DP=18;QA=684;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv1948c|Rv1948c|transcript|Rv1948c|protein_coding|1/1|c.13C>G|p.Arg5Gly|13/351|13/351|5/116||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:684:-61.8942,-5.41854,0
Chromosome	2199416	.	G	A	464.395	.	AB=0;AO=15;DP=15;QA=542;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv1948c-Rv1950c|Rv1948c-Rv1950c|intergenic_region|Rv1948c-Rv1950c|||n.2199416G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:542:-49.1095,-4.51545,0
Chromosome	2202833	.	G	A	609.356	.	AB=0;AO=20;DP=21;QA=739;QR=37;RO=1;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1957|Rv1957|transcript|Rv1957|protein_coding|1/1|c.250G>A|p.Asp84Asn|250/546|250/546|84/181||	GT:DP:RO:QR:AO:QA:GL	1/1:21:1:37:20:739:-63.1391,-2.6238,0
Chromosome	2203754	.	C	T	982.175	.	AB=0;AO=30;DP=30;QA=1129;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|parE1|Rv1959c|transcript|Rv1959c|protein_coding|1/1|c.224G>A|p.Arg75Gln|224/297|224/297|75/98||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1129:-101.914,-9.0309,0
Chromosome	2204260	.	A	G	502.916	.	AB=0;AO=17;DP=17;QA=583;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv1961|Rv1961|transcript|Rv1961|protein_coding|1/1|c.49A>G|p.Ser17Gly|49/495|49/495|17/164||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:583:-52.7799,-5.11751,0
Chromosome	2207591	.	T	TC	451.139	.	AB=0;AO=16;DP=16;QA=526;QR=0;RO=0;TYPE=ins;ANN=TC|intergenic_region|MODIFIER|mce3R-yrbE3A|Rv1963c-Rv1964|intergenic_region|Rv1963c-Rv1964|||n.2207591_2207592insC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:526:-47.6467,-4.81648,0
Chromosome	2209465	.	A	G	524.619	.	AB=0;AO=17;DP=17;QA=617;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mce3A|Rv1966|transcript|Rv1966|protein_coding|1/1|c.139A>G|p.Thr47Ala|139/1278|139/1278|47/425||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:617:-55.8601,-5.11751,0
Chromosome	2218012	.	G	A	809.522	.	AB=0;AO=26;DP=26;QA=927;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv1974|Rv1974|transcript|Rv1974|protein_coding|1/1|c.354G>A|p.Ala118Ala|354/378|354/378|118/125||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:927:-83.7376,-7.82678,0
Chromosome	2222308	.	C	T	754.799	.	AB=0;AO=26;DP=26;QA=870;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1979c|Rv1979c|transcript|Rv1979c|protein_coding|1/1|c.857G>A|p.Gly286Asp|857/1446|857/1446|286/481||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:870:-78.5926,-7.82678,0
Chromosome	2225456	.	A	T	807.293	.	AB=0;AO=25;DP=25;QA=925;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|vapC36|Rv1982c|transcript|Rv1982c|protein_coding|1/1|c.377T>A|p.Leu126His|377/420|377/420|126/139||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:925:-83.5643,-7.52575,0
Chromosome	2225882	.	G	A	609.876	.	AB=0;AO=19;DP=19;QA=702;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|vapB36|Rv1982A|transcript|Rv1982A|protein_coding|1/1|c.220C>T|p.Arg74Cys|220/261|220/261|74/86||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:702:-63.5111,-5.71957,0
Chromosome	2229801	.	G	C	728.181	.	AB=0;AO=24;DP=24;QA=847;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1985c|Rv1985c|transcript|Rv1985c|protein_coding|1/1|c.102C>G|p.Pro34Pro|102/912|102/912|34/303||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:847:-76.544,-7.22472,0
Chromosome	2231486	.	G	A	1114.24	.	AB=0;AO=37;DP=37;QA=1276;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv1987-erm(37)|Rv1987-Rv1988|intergenic_region|Rv1987-Rv1988|||n.2231486G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1276:-115.113,-11.1381,0
Chromosome	2233751	.	G	C	684.338	.	AB=0;AO=22;DP=22;QA=808;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv1990c-mazF6|Rv1990c-Rv1991c|intergenic_region|Rv1990c-Rv1991c|||n.2233751G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:808:-73.0441,-6.62266,0
Chromosome	2239349	.	G	A	615.393	.	AB=0;AO=20;DP=20;QA=710;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv1996|Rv1996|transcript|Rv1996|protein_coding|1/1|c.346G>A|p.Ala116Thr|346/954|346/954|116/317||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:710:-64.2199,-6.0206,0
Chromosome	2241742	.	G	A	522.758	.	AB=0;AO=17;DP=17;QA=606;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ctpF|Rv1997|transcript|Rv1997|protein_coding|1/1|c.1584G>A|p.Pro528Pro|1584/2718|1584/2718|528/905||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:606:-54.8611,-5.11751,0
Chromosome	2243034	.	G	T	957.085	.	AB=0;AO=31;DP=31;QA=1102;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv1998c|Rv1998c|transcript|Rv1998c|protein_coding|1/1|c.688C>A|p.Arg230Ser|688/777|688/777|230/258||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1102:-99.4842,-9.33193,0
Chromosome	2246960	.	C	G	842.892	.	AB=0;AO=30;DP=30;QA=970;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv2001|Rv2001|transcript|Rv2001|protein_coding|1/1|c.129C>G|p.Val43Val|129/753|129/753|43/250||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:970:-87.5789,-9.0309,0
Chromosome	2248179	.	A	G	618.791	.	AB=0;AO=19;DP=19;QA=709;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|fabG3|Rv2002|transcript|Rv2002|protein_coding|1/1|c.520A>G|p.Ser174Gly|520/783|520/783|174/260||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:709:-64.1411,-5.71957,0
Chromosome	2253453	.	T	C	923.927	.	AB=0;AO=29;DP=29;QA=1059;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|otsB1|Rv2006|transcript|Rv2006|protein_coding|1/1|c.1452T>C|p.Arg484Arg|1452/3984|1452/3984|484/1327||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1059:-95.6145,-8.72987,0
Chromosome	2260100	.	T	C	745.072	.	AB=0;AO=24;DP=24;QA=861;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv2012-Rv2015c|Rv2012-Rv2015c|intergenic_region|Rv2012-Rv2015c|||n.2260100T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:861:-77.801,-7.22472,0
Chromosome	2263760	.	C	T	454.845	.	AB=0;AO=16;DP=16;QA=529;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2016|Rv2016|transcript|Rv2016|protein_coding|1/1|c.335C>T|p.Pro112Leu|335/576|335/576|112/191||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:529:-47.9135,-4.81648,0
Chromosome	2282376	.	TT	CC	449.86	.	AB=0;AO=15;DP=15;QA=532;QR=0;RO=0;TYPE=complex;ANN=CC|missense_variant|MODERATE|Rv2036|Rv2036|transcript|Rv2036|protein_coding|1/1|c.278_279delTTinsCC|p.Val93Ala|278/642|278/642|93/213||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:532:-47.8779,-4.51545,0
Chromosome	2301089	.	C	T	444.518	.	AB=0;AO=14;DP=14;QA=516;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|pks12|Rv2048c|transcript|Rv2048c|protein_coding|1/1|c.5898G>A|p.Leu1966Leu|5898/12456|5898/12456|1966/4151||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:516:-46.7805,-4.21442,0
Chromosome	2307701	.	G	A	544.995	.	AB=0;AO=18;DP=18;QA=631;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv2049c-Rv2050|Rv2049c-Rv2050|intergenic_region|Rv2049c-Rv2050|||n.2307701G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:631:-57.1085,-5.41854,0
Chromosome	2325009	.	C	T	442.606	.	AB=0;AO=15;DP=15;QA=523;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2067c|Rv2067c|transcript|Rv2067c|protein_coding|1/1|c.862G>A|p.Glu288Lys|862/1224|862/1224|288/407||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:523:-47.3858,-4.51545,0
Chromosome	2328543	.	C	T	791.776	.	AB=0;AO=25;DP=25;QA=917;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|cobM|Rv2071c|transcript|Rv2071c|protein_coding|1/1|c.435G>A|p.Met145Ile|435/756|435/756|145/251||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:917:-82.8426,-7.52575,0
Chromosome	2330324	.	G	A	765.656	.	AB=0;AO=25;DP=25;QA=875;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2073c|Rv2073c|transcript|Rv2073c|protein_coding|1/1|c.640C>T|p.Arg214Cys|640/750|640/750|214/249||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:875:-79.0617,-7.52575,0
Chromosome	2331620	.	C	A	681.674	.	AB=0;AO=23;DP=23;QA=791;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2075c|Rv2075c|transcript|Rv2075c|protein_coding|1/1|c.1260G>T|p.Gly420Gly|1260/1464|1260/1464|420/487||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:791:-71.499,-6.92369,0
Chromosome	2331789	.	T	G	434.748	.	AB=0;AO=14;DP=14;QA=516;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2075c|Rv2075c|transcript|Rv2075c|protein_coding|1/1|c.1091A>C|p.Gln364Pro|1091/1464|1091/1464|364/487||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:516:-46.7779,-4.21442,0
Chromosome	2338768	.	G	T	749.905	.	AB=0;AO=24;DP=24;QA=857;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2082|Rv2082|transcript|Rv2082|protein_coding|1/1|c.60G>T|p.Pro20Pro|60/2166|60/2166|20/721||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:857:-77.4381,-7.22472,0
Chromosome	2338773	.	G	A	719.195	.	AB=0;AO=23;DP=23;QA=822;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2082|Rv2082|transcript|Rv2082|protein_coding|1/1|c.65G>A|p.Arg22Gln|65/2166|65/2166|22/721||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:822:-74.2976,-6.92369,0
Chromosome	2338961	.	G	A	720.382	.	AB=0;AO=23;DP=24;QA=829;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2082|Rv2082|transcript|Rv2082|protein_coding|1/1|c.253G>A|p.Val85Ile|253/2166|253/2166|85/721||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:23:829:-74.5614,-6.92369,0
Chromosome	2341030	.	A	G	844.125	.	AB=0;AO=27;DP=27;QA=981;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2083|Rv2083|transcript|Rv2083|protein_coding|1/1|c.160A>G|p.Thr54Ala|160/945|160/945|54/314||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:981:-88.5972,-8.12781,0
Chromosome	2368564	.	TA	T	517.771	.	AB=0;AO=20;DP=21;QA=607;QR=0;RO=0;TYPE=del;ANN=T|intergenic_region|MODIFIER|PPE36-prcA|Rv2108-Rv2109c|intergenic_region|Rv2108-Rv2109c|||n.2368565delA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:20:607:-54.624,-6.0206,0
Chromosome	2369186	.	C	G	939.865	.	AB=0;AO=30;DP=30;QA=1082;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|prcA|Rv2109c|transcript|Rv2109c|protein_coding|1/1|c.544G>C|p.Gly182Arg|544/747|544/747|182/248||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1082:-97.6827,-9.0309,0
Chromosome	2370533	.	A	C	848.732	.	AB=0;AO=27;DP=27;QA=979;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|prcB|Rv2110c|transcript|Rv2110c|protein_coding|1/1|c.69T>G|p.Ser23Ser|69/876|69/876|23/291||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:979:-88.4194,-8.12781,0
Chromosome	2376425	.	G	A	559.321	.	AB=0;AO=18;DP=18;QA=651;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|mpa-lppK|Rv2115c-Rv2116|intergenic_region|Rv2115c-Rv2116|||n.2376425G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:651:-58.9136,-5.41854,0
Chromosome	2379743	.	G	C	619.959	.	AB=0;AO=20;DP=21;QA=727;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv2120c-hisG|Rv2120c-Rv2121c|intergenic_region|Rv2120c-Rv2121c|||n.2379743G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:20:727:-65.5418,-6.0206,0
Chromosome	2388641	.	A	G	1123.97	.	AB=0;AO=36;DP=36;QA=1285;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ansP1|Rv2127|transcript|Rv2127|protein_coding|1/1|c.26A>G|p.Asp9Gly|26/1470|26/1470|9/489||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1285:-115.942,-10.8371,0
Chromosome	2390299	.	G	A	767.382	.	AB=0;AO=25;DP=25;QA=877;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv2128-Rv2129c|Rv2128-Rv2129c|intergenic_region|Rv2128-Rv2129c|||n.2390299G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:877:-79.2343,-7.52575,0
Chromosome	2396883	.	G	A	659.912	.	AB=0;AO=21;DP=21;QA=759;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv2136c-Rv2137c|Rv2136c-Rv2137c|intergenic_region|Rv2136c-Rv2137c|||n.2396883G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:759:-68.6318,-6.32163,0
Chromosome	2413246	.	A	C	720.341	.	AB=0;AO=23;DP=23;QA=844;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|murG|Rv2153c|transcript|Rv2153c|protein_coding|1/1|c.106T>G|p.Leu36Val|106/1233|106/1233|36/410||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:844:-76.2807,-6.92369,0
Chromosome	2416156	.	G	A	456.78	.	AB=0;AO=17;DP=17;QA=533;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|murD|Rv2155c|transcript|Rv2155c|protein_coding|1/1|c.239C>T|p.Thr80Ile|239/1461|239/1461|80/486||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:533:-48.2633,-5.11751,0
Chromosome	2421816	.	G	A	733.664	.	AB=0;AO=24;DP=24;QA=842;QR=0;RO=0;TYPE=snp;ANN=A|intragenic_variant|MODIFIER|Rv2160c|Rv2160c|gene_variant|Rv2160c|||n.2421816G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:842:-76.0948,-7.22472,0
Chromosome	2424864	.	G	A	334.929	.	AB=0;AO=11;DP=11;QA=412;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|PE_PGRS38-pbpB|Rv2162c-Rv2163c|intergenic_region|Rv2162c-Rv2163c|||n.2424864G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:412:-37.4277,-3.31133,0
Chromosome	2425471	.	C	T	768.101	.	AB=0;AO=25;DP=25;QA=880;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|pbpB|Rv2163c|transcript|Rv2163c|protein_coding|1/1|c.1617G>A|p.Arg539Arg|1617/2040|1617/2040|539/679||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:880:-79.5079,-7.52575,0
Chromosome	2426630	.	C	T	290.605	.	AB=0;AO=11;DP=11;QA=346;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|pbpB|Rv2163c|transcript|Rv2163c|protein_coding|1/1|c.458G>A|p.Arg153His|458/2040|458/2040|153/679||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:346:-31.439,-3.31133,0
Chromosome	2437259	.	T	G	658.459	.	AB=0;AO=21;DP=21;QA=761;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mptA|Rv2174|transcript|Rv2174|protein_coding|1/1|c.1351T>G|p.Ser451Ala|1351/1551|1351/1551|451/516||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:761:-68.8088,-6.32163,0
Chromosome	2438955	.	G	A	553.856	.	AB=0;AO=18;DP=18;QA=646;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|pknL|Rv2176|transcript|Rv2176|protein_coding|1/1|c.1015G>A|p.Gly339Arg|1015/1200|1015/1200|339/399||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:646:-58.4628,-5.41854,0
Chromosome	2441590	.	T	C	493.816	.	AB=0;AO=17;DP=17;QA=575;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|aroG|Rv2178c|transcript|Rv2178c|protein_coding|1/1|c.131A>G|p.Gln44Arg|131/1389|131/1389|44/462||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:575:-52.0638,-5.11751,0
Chromosome	2447539	.	G	A	753.535	.	AB=0;AO=24;DP=24;QA=868;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|TB16.3-Rv2186c|Rv2185c-Rv2186c|intergenic_region|Rv2185c-Rv2186c|||n.2447539G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:868:-78.4366,-7.22472,0
Chromosome	2448458	.	T	C	342.274	.	AB=0;AO=11;DP=11;QA=403;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|fadD15|Rv2187|transcript|Rv2187|protein_coding|1/1|c.299T>C|p.Ile100Thr|299/1803|299/1803|100/600||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:403:-36.6146,-3.31133,0
Chromosome	2449284	.	C	T	674.396	.	AB=0;AO=22;DP=22;QA=773;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|fadD15|Rv2187|transcript|Rv2187|protein_coding|1/1|c.1125C>T|p.Tyr375Tyr|1125/1803|1125/1803|375/600||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:773:-69.8756,-6.62266,0
Chromosome	2449295	.	A	G	686.938	.	AB=0;AO=22;DP=22;QA=786;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|fadD15|Rv2187|transcript|Rv2187|protein_coding|1/1|c.1136A>G|p.Glu379Gly|1136/1803|1136/1803|379/600||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:786:-71.0542,-6.62266,0
Chromosome	2454856	.	C	T	722.328	.	AB=0;AO=23;DP=23;QA=832;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2191|Rv2191|transcript|Rv2191|protein_coding|1/1|c.1038C>T|p.Arg346Arg|1038/1938|1038/1938|346/645||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:832:-75.1965,-6.92369,0
Chromosome	2460628	.	C	A	720.186	.	AB=0;AO=24;DP=24;QA=824;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|qcrB|Rv2196|transcript|Rv2196|protein_coding|1/1|c.951C>A|p.Ala317Ala|951/1650|951/1650|317/549||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:824:-74.4662,-7.22472,0
Chromosome	2470591	.	C	A	391.223	.	AB=0;AO=13;DP=14;QA=484;QR=14;RO=1;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv2205c-Rv2206|Rv2205c-Rv2206|intergenic_region|Rv2205c-Rv2206|||n.2470591C>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:1:14:13:484:-42.5014,-2.81443,0
Chromosome	2472956	.	C	T	956.279	.	AB=0;AO=30;DP=30;QA=1095;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|cobS|Rv2208|transcript|Rv2208|protein_coding|1/1|c.464C>T|p.Ser155Leu|464/750|464/750|155/249||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1095:-98.8555,-9.0309,0
Chromosome	2475207	.	G	A	710.85	.	AB=0;AO=23;DP=23;QA=816;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ilvE|Rv2210c|transcript|Rv2210c|protein_coding|1/1|c.764C>T|p.Ser255Leu|764/1107|764/1107|255/368||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:816:-73.7543,-6.92369,0
Chromosome	2487490	.	AG	A	293.307	.	AB=0;AO=10;DP=10;QA=347;QR=0;RO=0;TYPE=del;ANN=A|intergenic_region|MODIFIER|Rv2219A-glnA1|Rv2219A-Rv2220|intergenic_region|Rv2219A-Rv2220|||n.2487491delG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:347:-31.5588,-3.0103,0
Chromosome	2495500	.	C	T	761.76	.	AB=0;AO=25;DP=25;QA=873;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|caeA|Rv2224c|transcript|Rv2224c|protein_coding|1/1|c.1524G>A|p.Leu508Leu|1524/1563|1524/1563|508/520||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:873:-78.8738,-7.52575,0
Chromosome	2501148	.	C	T	736.011	.	AB=0;AO=24;DP=24;QA=854;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2227|Rv2227|transcript|Rv2227|protein_coding|1/1|c.218C>T|p.Ala73Val|218/702|218/702|73/233||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:854:-77.1758,-7.22472,0
Chromosome	2506888	.	T	G	956.904	.	AB=0;AO=31;DP=31;QA=1092;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ptkA|Rv2232|transcript|Rv2232|protein_coding|1/1|c.611T>G|p.Val204Gly|611/876|611/876|204/291||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1092:-98.5808,-9.33193,0
Chromosome	2511712	.	T	G	818.038	.	AB=0;AO=26;DP=26;QA=943;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2240c|Rv2240c|transcript|Rv2240c|protein_coding|1/1|c.569A>C|p.Lys190Thr|569/591|569/591|190/196||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:943:-85.1762,-7.82678,0
Chromosome	2512237	.	T	TC	507.518	.	AB=0;AO=17;DP=17;QA=588;QR=0;RO=0;TYPE=ins;ANN=TC|frameshift_variant|HIGH|Rv2240c|Rv2240c|transcript|Rv2240c|protein_coding|1/1|c.43dupG|p.Glu15fs|43/591|43/591|15/196||;LOF=(Rv2240c|Rv2240c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:588:-53.2402,-5.11751,0
Chromosome	2518132	.	T	C	612.56	.	AB=0;AO=19;DP=19;QA=708;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|kasA|Rv2245|transcript|Rv2245|protein_coding|1/1|c.18T>C|p.Thr6Thr|18/1251|18/1251|6/416||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:708:-64.0501,-5.71957,0
Chromosome	2523205	.	G	GCGC	299.082	.	AB=0;AO=11;DP=12;QA=364;QR=0;RO=0;TYPE=ins;ANN=GCGC|intergenic_region|MODIFIER|Rv2248-glpD1|Rv2248-Rv2249c|intergenic_region|Rv2248-Rv2249c|||n.2523205_2523206insCGC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:11:364:-32.7726,-3.31133,0
Chromosome	2525722	.	CG	C	755.387	.	AB=0;AO=24;DP=24;QA=863;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv2251|Rv2251|transcript|Rv2251|protein_coding|1/1|c.163delG|p.Glu55fs|163/1428|163/1428|55/475||INFO_REALIGN_3_PRIME;LOF=(Rv2251|Rv2251|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:863:-77.9863,-7.22472,0
Chromosome	2526026	.	G	A	646.817	.	AB=0;AO=21;DP=21;QA=749;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2251|Rv2251|transcript|Rv2251|protein_coding|1/1|c.462G>A|p.Ala154Ala|462/1428|462/1428|154/475||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:749:-67.7251,-6.32163,0
Chromosome	2527120	.	C	T	687.858	.	AB=0;AO=23;DP=23;QA=793;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2252|Rv2252|transcript|Rv2252|protein_coding|1/1|c.132C>T|p.Asp44Asp|132/930|132/930|44/309||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:793:-71.6769,-6.92369,0
Chromosome	2534561	.	CGG	C	481.717	.	AB=0;AO=17;DP=17;QA=575;QR=0;RO=0;TYPE=del;ANN=C|intragenic_variant|MODIFIER|Rv2261c|Rv2261c|gene_variant|Rv2261c|||n.2534562_2534563delGG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:575:-52.0673,-5.11751,0
Chromosome	2537780	.	G	A	552.542	.	AB=0;AO=17;DP=17;QA=640;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2264c|Rv2264c|transcript|Rv2264c|protein_coding|1/1|c.571C>T|p.Arg191Trp|571/1779|571/1779|191/592||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:640:-57.9364,-5.11751,0
Chromosome	2540326	.	T	A	395.147	.	AB=0;AO=13;DP=13;QA=458;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|cyp124|Rv2266|transcript|Rv2266|protein_coding|1/1|c.223T>A|p.Tyr75Asn|223/1287|223/1287|75/428||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:458:-41.5513,-3.91339,0
Chromosome	2557095	.	G	T	646.718	.	AB=0;AO=20;DP=20;QA=741;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|lipM|Rv2284|transcript|Rv2284|protein_coding|1/1|c.951G>T|p.Leu317Leu|951/1296|951/1296|317/431||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:741:-67.0166,-6.0206,0
Chromosome	2559686	.	C	T	764.368	.	AB=0;AO=24;DP=24;QA=873;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv2286c-yjcE|Rv2286c-Rv2287|intergenic_region|Rv2286c-Rv2287|||n.2559686C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:873:-78.8844,-7.22472,0
Chromosome	2562783	.	C	T	537.836	.	AB=0;AO=18;DP=18;QA=620;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|lppO|Rv2290|transcript|Rv2290|protein_coding|1/1|c.185C>T|p.Ala62Val|185/516|185/516|62/171||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:620:-56.116,-5.41854,0
Chromosome	2563958	.	C	A	951.633	.	AB=0;AO=31;DP=31;QA=1088;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|sseB|Rv2291|transcript|Rv2291|protein_coding|1/1|c.785C>A|p.Ala262Glu|785/855|785/855|262/284||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1088:-98.2172,-9.33193,0
Chromosome	2566768	.	G	A	374.374	.	AB=0;AO=13;DP=13;QA=488;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv2294-Rv2295|Rv2294-Rv2295|intergenic_region|Rv2294-Rv2295|||n.2566768G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:488:-44.2648,-3.91339,0
Chromosome	2574022	.	C	T	507.9	.	AB=0;AO=17;DP=17;QA=594;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2302|Rv2302|transcript|Rv2302|protein_coding|1/1|c.210C>T|p.Arg70Arg|210/243|210/243|70/80||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:594:-53.7732,-5.11751,0
Chromosome	2577246	.	G	A	869.987	.	AB=0;AO=29;DP=29;QA=994;QR=0;RO=0;TYPE=snp;ANN=A|intragenic_variant|MODIFIER|Rv2306A|Rv2306A|gene_variant|Rv2306A|||n.2577246G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:994:-89.752,-8.72987,0
Chromosome	2577461	.	C	G	680.004	.	AB=0;AO=22;DP=22;QA=785;QR=0;RO=0;TYPE=snp;ANN=G|intragenic_variant|MODIFIER|Rv2306A|Rv2306A|gene_variant|Rv2306A|||n.2577461C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:785:-70.9701,-6.62266,0
Chromosome	2580954	.	G	C	1116.48	.	AB=0;AO=34;DP=34;QA=1272;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2308|Rv2308|transcript|Rv2308|protein_coding|1/1|c.536G>C|p.Arg179Pro|536/717|536/717|179/238||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1272:-114.774,-10.235,0
Chromosome	2581109	.	A	C	544.487	.	AB=0;AO=17;DP=17;QA=630;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2308|Rv2308|transcript|Rv2308|protein_coding|1/1|c.691A>C|p.Arg231Arg|691/717|691/717|231/238||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:630:-57.034,-5.11751,0
Chromosome	2582348	.	G	T	868.936	.	AB=0;AO=28;DP=28;QA=997;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|metV-Rv2309A|Rvnt24-Rv2309A|intergenic_region|Rvnt24-Rv2309A|||n.2582348G>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:997:-90.0331,-8.42884,0
Chromosome	2585809	.	G	A	1038.79	.	AB=0;AO=37;DP=37;QA=1196;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2313c|Rv2313c|transcript|Rv2313c|protein_coding|1/1|c.98C>T|p.Ala33Val|98/855|98/855|33/284||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1196:-107.913,-11.1381,0
Chromosome	2603797	.	G	A	738.651	.	AB=0;AO=23;DP=23;QA=861;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|lppP|Rv2330c|transcript|Rv2330c|protein_coding|1/1|c.426C>T|p.Ile142Ile|426/528|426/528|142/175||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:861:-77.8106,-6.92369,0
Chromosome	2605293	.	T	G	483.596	.	AB=0;AO=16;DP=16;QA=570;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|mez|Rv2332|transcript|Rv2332|protein_coding|1/1|c.186T>G|p.Asp62Glu|186/1647|186/1647|62/548||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:570:-51.625,-4.81648,0
Chromosome	2608488	.	C	T	767.015	.	AB=0;AO=24;DP=24;QA=887;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|stp-cysK1|Rv2333c-Rv2334|intergenic_region|Rv2333c-Rv2334|||n.2608488C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:887:-80.1466,-7.22472,0
Chromosome	2610702	.	T	C	781.224	.	AB=0;AO=25;DP=25;QA=909;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|cysE-Rv2336|Rv2335-Rv2336|intergenic_region|Rv2335-Rv2336|||n.2610702T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:909:-82.1171,-7.52575,0
Chromosome	2611891	.	T	A	650.848	.	AB=0;AO=21;DP=21;QA=758;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2337c|Rv2337c|transcript|Rv2337c|protein_coding|1/1|c.1097A>T|p.Asp366Val|1097/1119|1097/1119|366/372||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:758:-68.5384,-6.32163,0
Chromosome	2617673	.	G	A	920.626	.	AB=0;AO=30;DP=30;QA=1053;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|PE_PGRS39|Rv2340c|transcript|Rv2340c|protein_coding|1/1|c.1236C>T|p.His412His|1236/1242|1236/1242|412/413||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1053:-95.0646,-9.0309,0
Chromosome	2619271	.	C	T	853.612	.	AB=0;AO=28;DP=28;QA=980;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|PE_PGRS39-asnT|Rv2340c-Rvnt25|intergenic_region|Rv2340c-Rvnt25|||n.2619271C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:980:-88.5007,-8.42884,0
Chromosome	2623232	.	C	G	945.756	.	AB=0;AO=29;DP=29;QA=1078;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|dgt|Rv2344c|transcript|Rv2344c|protein_coding|1/1|c.521G>C|p.Gly174Ala|521/1296|521/1296|174/431||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1078:-97.3288,-8.72987,0
Chromosome	2625924	.	C	T	419.573	.	AB=0;AO=13;DP=13;QA=485;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|esxO|Rv2346c|transcript|Rv2346c|protein_coding|1/1|c.249G>A|p.Ala83Ala|249/285|249/285|83/94||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:485:-43.9939,-3.91339,0
Chromosome	2626189	.	AGT	CGC	587.105	.	AB=0;AO=20;DP=20;QA=736;QR=0;RO=0;TYPE=complex;ANN=CGC|intergenic_region|MODIFIER|esxO-esxP|Rv2346c-Rv2347c|intergenic_region|Rv2346c-Rv2347c|||n.2626189_2626191delAGTinsCGC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:736:-66.3219,-6.0206,0
Chromosome	2631641	.	G	T	563.251	.	AB=0;AO=18;DP=18;QA=664;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|plcA|Rv2351c|transcript|Rv2351c|protein_coding|1/1|c.435C>A|p.Pro145Pro|435/1539|435/1539|145/512||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:664:-60.0895,-5.41854,0
Chromosome	2632500	.	G	A	775.553	.	AB=0;AO=24;DP=24;QA=894;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|plcA-PPE38|Rv2351c-Rv2352c|intergenic_region|Rv2351c-Rv2352c|||n.2632500G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:894:-80.7778,-7.22472,0
Chromosome	2641840	.	G	A	712.035	.	AB=0;AO=24;DP=24;QA=815;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|zur|Rv2359|transcript|Rv2359|protein_coding|1/1|c.191G>A|p.Arg64His|191/393|191/393|64/130||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:815:-73.6511,-7.22472,0
Chromosome	2645270	.	C	T	908.347	.	AB=0;AO=29;DP=29;QA=1045;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|amiA2|Rv2363|transcript|Rv2363|protein_coding|1/1|c.951C>T|p.Gly317Gly|951/1455|951/1455|317/484||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1045:-94.352,-8.72987,0
Chromosome	2652174	.	C	A	502.546	.	AB=0;AO=17;DP=17;QA=624;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2372c|Rv2372c|transcript|Rv2372c|protein_coding|1/1|c.652G>T|p.Val218Phe|652/789|652/789|218/262||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:624:-56.4925,-5.11751,0
Chromosome	2655691	.	T	C	742.067	.	AB=0;AO=25;DP=25;QA=871;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|cfp2|Rv2376c|transcript|Rv2376c|protein_coding|1/1|c.425A>G|p.Gln142Arg|425/507|425/507|142/168||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:871:-78.6935,-7.52575,0
Chromosome	2660091	.	T	G	974.91	.	AB=0;AO=32;DP=32;QA=1112;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|mbtF|Rv2379c|transcript|Rv2379c|protein_coding|1/1|c.1995A>C|p.Ala665Ala|1995/4386|1995/4386|665/1461||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1112:-100.37,-9.63296,0
Chromosome	2671061	.	C	A	419.212	.	AB=0;AO=13;DP=13;QA=486;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|mbtC|Rv2382c|transcript|Rv2382c|protein_coding|1/1|c.543G>T|p.Ala181Ala|543/1335|543/1335|181/444||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:486:-44.0827,-3.91339,0
Chromosome	2691713	.	C	T	688.465	.	AB=0;AO=22;DP=22;QA=791;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2395|Rv2395|transcript|Rv2395|protein_coding|1/1|c.1642C>T|p.Pro548Ser|1642/2004|1642/2004|548/667||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:791:-71.5104,-6.62266,0
Chromosome	2700239	.	G	A	988.972	.	AB=0;AO=32;DP=33;QA=1165;QR=39;RO=1;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2402|Rv2402|transcript|Rv2402|protein_coding|1/1|c.1711G>A|p.Val571Met|1711/1929|1711/1929|571/642||	GT:DP:RO:QR:AO:QA:GL	1/1:33:1:39:32:1165:-101.251,-6.03743,0
Chromosome	2709795	.	G	A	575.441	.	AB=0;AO=19;DP=19;QA=663;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2411c|Rv2411c|transcript|Rv2411c|protein_coding|1/1|c.171C>T|p.Ala57Ala|171/1656|171/1656|57/551||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:663:-59.9804,-5.71957,0
Chromosome	2712913	.	A	C	916.414	.	AB=0;AO=29;DP=29;QA=1048;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2415c|Rv2415c|transcript|Rv2415c|protein_coding|1/1|c.872T>G|p.Leu291Arg|872/894|872/894|291/297||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1048:-94.6286,-8.72987,0
Chromosome	2723506	.	C	T	674.007	.	AB=0;AO=21;DP=21;QA=772;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2426c|Rv2426c|transcript|Rv2426c|protein_coding|1/1|c.678G>A|p.Leu226Leu|678/876|678/876|226/291||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:772:-69.8025,-6.32163,0
Chromosome	2730752	.	T	C	949.969	.	AB=0;AO=29;DP=29;QA=1084;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2435c|Rv2435c|transcript|Rv2435c|protein_coding|1/1|c.1998A>G|p.Ser666Ser|1998/2193|1998/2193|666/730||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1084:-97.8682,-8.72987,0
Chromosome	2739174	.	T	G	421.377	.	AB=0;AO=13;DP=13;QA=487;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|obg|Rv2440c|transcript|Rv2440c|protein_coding|1/1|c.513A>C|p.Gly171Gly|513/1440|513/1440|171/479||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:487:-44.1744,-3.91339,0
Chromosome	2740693	.	C	T	525.577	.	AB=0;AO=19;DP=19;QA=624;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|rplU-dctA|Rv2442c-Rv2443|intergenic_region|Rv2442c-Rv2443|||n.2740693C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:624:-56.4601,-5.71957,0
Chromosome	2752854	.	G	A	746.377	.	AB=0;AO=23;DP=23;QA=862;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2452c|Rv2452c|transcript|Rv2452c|protein_coding|1/1|c.141C>T|p.Asp47Asp|141/147|141/147|47/48||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:862:-77.9024,-6.92369,0
Chromosome	2759082	.	T	G	657.486	.	AB=0;AO=21;DP=21;QA=759;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|clpX|Rv2457c|transcript|Rv2457c|protein_coding|1/1|c.407A>C|p.Lys136Thr|407/1281|407/1281|136/426||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:759:-68.6323,-6.32163,0
Chromosome	2760241	.	G	A	461.446	.	AB=0;AO=17;DP=18;QA=567;QR=39;RO=1;TYPE=snp;ANN=A|missense_variant|MODERATE|mmuM|Rv2458|transcript|Rv2458|protein_coding|1/1|c.463G>A|p.Glu155Lys|463/909|463/909|155/302||	GT:DP:RO:QR:AO:QA:GL	1/1:18:1:39:17:567:-47.4367,-1.52198,0
Chromosome	2760985	.	G	T	869.236	.	AB=0;AO=28;DP=28;QA=1005;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2459|Rv2459|transcript|Rv2459|protein_coding|1/1|c.132G>T|p.Leu44Leu|132/1527|132/1527|44/508||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1005:-90.7512,-8.42884,0
Chromosome	2772619	.	G	C	1133.47	.	AB=0;AO=36;DP=36;QA=1286;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2469c|Rv2469c|transcript|Rv2469c|protein_coding|1/1|c.417C>G|p.Ala139Ala|417/669|417/669|139/222||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1286:-116.031,-10.8371,0
Chromosome	2773931	.	T	C	773.517	.	AB=0;AO=25;DP=25;QA=899;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|aglA|Rv2471|transcript|Rv2471|protein_coding|1/1|c.368T>C|p.Met123Thr|368/1641|368/1641|123/546||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:899:-81.2208,-7.52575,0
Chromosome	2788745	.	C	T	838.538	.	AB=0;AO=26;DP=26;QA=957;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|plsB2|Rv2482c|transcript|Rv2482c|protein_coding|1/1|c.539G>A|p.Arg180Gln|539/2370|539/2370|180/789||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:957:-86.4442,-7.82678,0
Chromosome	2790458	.	C	A	515.974	.	AB=0;AO=16;DP=16;QA=600;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|plsC|Rv2483c|transcript|Rv2483c|protein_coding|1/1|c.565G>T|p.Gly189Cys|565/1743|565/1743|189/580||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:600:-54.3363,-4.81648,0
Chromosome	2791098	.	T	C	441.109	.	AB=0;AO=16;DP=16;QA=553;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2484c|Rv2484c|transcript|Rv2484c|protein_coding|1/1|c.1397A>G|p.Asp466Gly|1397/1476|1397/1476|466/491||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:553:-50.0927,-4.81648,0
Chromosome	2791475	.	G	A	567.599	.	AB=0;AO=20;DP=20;QA=659;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2484c|Rv2484c|transcript|Rv2484c|protein_coding|1/1|c.1020C>T|p.Ala340Ala|1020/1476|1020/1476|340/491||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:659:-59.6069,-6.0206,0
Chromosome	2807486	.	A	C	650.788	.	AB=0;AO=22;DP=22;QA=758;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2492|Rv2492|transcript|Rv2492|protein_coding|1/1|c.209A>C|p.Asp70Ala|209/753|209/753|70/250||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:758:-68.5288,-6.62266,0
Chromosome	2808506	.	G	C	709.68	.	AB=0;AO=22;DP=22;QA=812;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|vapC38|Rv2494|transcript|Rv2494|protein_coding|1/1|c.197G>C|p.Arg66Pro|197/426|197/426|66/141||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:812:-73.404,-6.62266,0
Chromosome	2825466	.	A	G	763.559	.	AB=0;AO=24;DP=24;QA=876;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv2509|Rv2509|transcript|Rv2509|protein_coding|1/1|c.789A>G|p.Lys263Lys|789/807|789/807|263/268||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:876:-79.1524,-7.22472,0
Chromosome	2841022	.	G	A	1101.36	.	AB=0;AO=35;DP=35;QA=1259;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|fas|Rv2524c|transcript|Rv2524c|protein_coding|1/1|c.8311C>T|p.Arg2771Cys|8311/9210|8311/9210|2771/3069||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1259:-113.606,-10.5361,0
Chromosome	2841238	.	C	A	935.226	.	AB=0;AO=30;DP=30;QA=1073;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|fas|Rv2524c|transcript|Rv2524c|protein_coding|1/1|c.8095G>T|p.Ala2699Ser|8095/9210|8095/9210|2699/3069||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1073:-96.8626,-9.0309,0
Chromosome	2843168	.	C	T	1066.71	.	AB=0;AO=35;DP=36;QA=1251;QR=38;RO=1;TYPE=snp;ANN=T|synonymous_variant|LOW|fas|Rv2524c|transcript|Rv2524c|protein_coding|1/1|c.6165G>A|p.Glu2055Glu|6165/9210|6165/9210|2055/3069||	GT:DP:RO:QR:AO:QA:GL	1/1:36:1:38:35:1251:-109.087,-7.03981,0
Chromosome	2847281	.	G	A	612.509	.	AB=0;AO=19;DP=19;QA=703;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|fas|Rv2524c|transcript|Rv2524c|protein_coding|1/1|c.2052C>T|p.Asp684Asp|2052/9210|2052/9210|684/3069||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:703:-63.6001,-5.71957,0
Chromosome	2858669	.	T	G	757.948	.	AB=0;AO=25;DP=25;QA=868;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|nusB|Rv2533c|transcript|Rv2533c|protein_coding|1/1|c.56A>C|p.Asp19Ala|56/471|56/471|19/156||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:868:-78.4257,-7.52575,0
Chromosome	2862052	.	C	T	395.997	.	AB=0;AO=13;DP=13;QA=459;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|aroB|Rv2538c|transcript|Rv2538c|protein_coding|1/1|c.625G>A|p.Ala209Thr|625/1089|625/1089|209/362||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:459:-41.6363,-3.91339,0
Chromosome	2870386	.	T	C	835.166	.	AB=0;AO=27;DP=27;QA=985;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|vapB20-Rv2551c|Rv2550c-Rv2551c|intergenic_region|Rv2550c-Rv2551c|||n.2870386T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:985:-88.9517,-8.12781,0
Chromosome	2871977	.	C	G	645.952	.	AB=0;AO=20;DP=20;QA=742;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|aroE|Rv2552c|transcript|Rv2552c|protein_coding|1/1|c.39G>C|p.Ser13Ser|39/810|39/810|13/269||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:742:-67.1064,-6.0206,0
Chromosome	2878980	.	T	C	564.852	.	AB=0;AO=18;DP=18;QA=653;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2559c|Rv2559c|transcript|Rv2559c|protein_coding|1/1|c.950A>G|p.Asp317Gly|950/1359|950/1359|317/452||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:653:-59.0985,-5.41854,0
Chromosome	2881597	.	AG	A	454.34	.	AB=0;AO=15;DP=15;QA=526;QR=0;RO=0;TYPE=del;ANN=A|intragenic_variant|MODIFIER|Rv2561|Rv2561|gene_variant|Rv2561|||n.2881598delG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:526:-47.6638,-4.51545,0
Chromosome	2885734	.	G	A	451.265	.	AB=0;AO=15;DP=15;QA=525;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2565|Rv2565|transcript|Rv2565|protein_coding|1/1|c.1124G>A|p.Gly375Asp|1124/1752|1124/1752|375/583||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:525:-47.5746,-4.51545,0
Chromosome	2886570	.	G	A	719.812	.	AB=0;AO=23;DP=23;QA=840;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2566|Rv2566|transcript|Rv2566|protein_coding|1/1|c.198G>A|p.Glu66Glu|198/3423|198/3423|66/1140||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:840:-75.9149,-6.92369,0
Chromosome	2897871	.	G	A	640.187	.	AB=0;AO=22;DP=22;QA=741;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|aspS-Rv2573|Rv2572c-Rv2573|intergenic_region|Rv2572c-Rv2573|||n.2897871G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:741:-66.9884,-6.62266,0
Chromosome	2913078	.	C	G	899.756	.	AB=0;AO=28;DP=28;QA=1034;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|secF|Rv2586c|transcript|Rv2586c|protein_coding|1/1|c.934G>C|p.Val312Leu|934/1329|934/1329|312/442||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1034:-93.3663,-8.42884,0
Chromosome	2917173	.	G	A	368.592	.	AB=0;AO=12;DP=12;QA=438;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|gabT|Rv2589|transcript|Rv2589|protein_coding|1/1|c.814G>A|p.Gly272Arg|814/1350|814/1350|272/449||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:438:-39.7605,-3.61236,0
Chromosome	2925962	.	C	T	1144.66	.	AB=0;AO=35;DP=35;QA=1312;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|vapC40|Rv2596|transcript|Rv2596|protein_coding|1/1|c.229C>T|p.Arg77Cys|229/405|229/405|77/134||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1312:-118.37,-10.5361,0
Chromosome	2927511	.	T	G	809.369	.	AB=0;AO=27;DP=27;QA=966;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2599|Rv2599|transcript|Rv2599|protein_coding|1/1|c.35T>G|p.Ile12Ser|35/432|35/432|12/143||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:966:-87.2496,-8.12781,0
Chromosome	2935682	.	C	A	416.412	.	AB=0;AO=14;DP=14;QA=489;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|PPE42|Rv2608|transcript|Rv2608|protein_coding|1/1|c.637C>A|p.Arg213Arg|637/1743|637/1743|213/580||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:489:-44.3289,-4.21442,0
Chromosome	2945042	.	C	G	593.988	.	AB=0;AO=20;DP=20;QA=740;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|PE_PGRS45-Rv2616|Rv2615c-Rv2616|intergenic_region|Rv2615c-Rv2616|||n.2945042C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:740:-66.9274,-6.0206,0
Chromosome	2946570	.	G	A	374.48	.	AB=0;AO=13;DP=13;QA=438;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2618|Rv2618|transcript|Rv2618|protein_coding|1/1|c.137G>A|p.Gly46Asp|137/678|137/678|46/225||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:438:-39.7345,-3.91339,0
Chromosome	2953307	.	T	G	573.633	.	AB=0;AO=19;DP=19;QA=660;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|hrp1-Rv2627c|Rv2626c-Rv2627c|intergenic_region|Rv2626c-Rv2627c|||n.2953307T>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:660:-59.7125,-5.71957,0
Chromosome	2953367	.	T	C	560.316	.	AB=0;AO=18;DP=18;QA=650;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|hrp1-Rv2627c|Rv2626c-Rv2627c|intergenic_region|Rv2626c-Rv2627c|||n.2953367T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:650:-58.8289,-5.41854,0
Chromosome	2955233	.	T	C	809.443	.	AB=0;AO=26;DP=26;QA=932;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2628|Rv2628|transcript|Rv2628|protein_coding|1/1|c.176T>C|p.Leu59Ser|176/363|176/363|59/120||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:932:-84.1876,-7.82678,0
Chromosome	2958749	.	G	A	1476.63	.	AB=0;AO=47;DP=47;QA=1674;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2631|Rv2631|transcript|Rv2631|protein_coding|1/1|c.1178G>A|p.Gly393Asp|1178/1299|1178/1299|393/432||	GT:DP:RO:QR:AO:QA:GL	1/1:47:0:0:47:1674:-150.922,-14.1484,0
Chromosome	2959324	.	G	A	926.817	.	AB=0;AO=30;DP=30;QA=1058;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv2632c-Rv2633c|Rv2632c-Rv2633c|intergenic_region|Rv2632c-Rv2633c|||n.2959324G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1058:-95.5122,-9.0309,0
Chromosome	2970017	.	CGA	GTG	426.027	.	AB=0;AO=14;DP=14;QA=507;QR=0;RO=0;TYPE=complex;ANN=GTG|intergenic_region|MODIFIER|valU-Rv2645|Rvnt34-Rv2645|intergenic_region|Rvnt34-Rv2645|||n.2970017_2970019delCGAinsGTG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:507:-45.6426,-4.21442,0
Chromosome	2971122	.	C	T	405.301	.	AB=0;AO=14;DP=14;QA=482;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2646|Rv2646|transcript|Rv2646|protein_coding|1/1|c.572C>T|p.Thr191Ile|572/999|572/999|191/332||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:482:-43.695,-4.21442,0
Chromosome	2975227	.	G	T	720.69	.	AB=0;AO=24;DP=24;QA=834;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2650c|Rv2650c|transcript|Rv2650c|protein_coding|1/1|c.8C>A|p.Thr3Asn|8/1440|8/1440|3/479||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:834:-75.3628,-7.22472,0
Chromosome	2976616	.	C	G	325.969	.	AB=0;AO=12;DP=12;QA=391;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2653c|Rv2653c|transcript|Rv2653c|protein_coding|1/1|c.294G>C|p.Gln98His|294/324|294/324|98/107||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:391:-35.4982,-3.61236,0
Chromosome	2980970	.	C	A	499.516	.	AB=0;AO=16;DP=16;QA=583;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2660c|Rv2660c|transcript|Rv2660c|protein_coding|1/1|c.221G>T|p.Cys74Phe|221/228|221/228|74/75||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:583:-52.7988,-4.81648,0
Chromosome	2985216	.	A	G	666.785	.	AB=0;AO=21;DP=21;QA=764;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2668|Rv2668|transcript|Rv2668|protein_coding|1/1|c.484A>G|p.Lys162Glu|484/522|484/522|162/173||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:764:-69.0803,-6.32163,0
Chromosome	2988630	.	G	C	357.69	.	AB=0;AO=12;DP=12;QA=431;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2672|Rv2672|transcript|Rv2672|protein_coding|1/1|c.949G>C|p.Asp317His|949/1587|949/1587|317/528||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:431:-39.1263,-3.61236,0
Chromosome	2994187	.	C	T	736.939	.	AB=0;AO=25;DP=25;QA=844;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|hemE|Rv2678c|transcript|Rv2678c|protein_coding|1/1|c.876G>A|p.Leu292Leu|876/1074|876/1074|292/357||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:844:-76.2569,-7.52575,0
Chromosome	3000362	.	C	T	919.895	.	AB=0;AO=28;DP=28;QA=1055;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2683|Rv2683|transcript|Rv2683|protein_coding|1/1|c.251C>T|p.Ser84Leu|251/498|251/498|84/165||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1055:-95.2601,-8.42884,0
Chromosome	3001395	.	T	C	863.855	.	AB=0;AO=28;DP=28;QA=986;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|arsA|Rv2684|transcript|Rv2684|protein_coding|1/1|c.782T>C|p.Val261Ala|782/1290|782/1290|261/429||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:986:-89.0421,-8.42884,0
Chromosome	3003115	.	G	C	502.284	.	AB=0;AO=16;DP=16;QA=586;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|arsB1|Rv2685|transcript|Rv2685|protein_coding|1/1|c.1133G>C|p.Gly378Ala|1133/1287|1133/1287|378/428||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:586:-53.0756,-4.81648,0
Chromosome	3005618	.	C	T	1131.9	.	AB=0;AO=36;DP=36;QA=1289;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2688c|Rv2688c|transcript|Rv2688c|protein_coding|1/1|c.33G>A|p.Ala11Ala|33/906|33/906|11/301||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1289:-116.3,-10.8371,0
Chromosome	3006898	.	A	G	1050.62	.	AB=0;AO=33;DP=33;QA=1193;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv2689c|Rv2689c|transcript|Rv2689c|protein_coding|1/1|c.165T>C|p.Tyr55Tyr|165/1218|165/1218|55/405||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1193:-107.663,-9.93399,0
Chromosome	3007238	.	G	A	763.781	.	AB=0;AO=25;DP=25;QA=876;QR=0;RO=0;TYPE=snp;ANN=A|stop_gained&splice_region_variant|HIGH|Rv2690c|Rv2690c|transcript|Rv2690c|protein_coding|1/1|c.1972C>T|p.Arg658*|1972/1974|1972/1974|658/657||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:876:-79.1428,-7.52575,0
Chromosome	3010420	.	G	A	683.716	.	AB=0;AO=22;DP=22;QA=790;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ceoC|Rv2692|transcript|Rv2692|protein_coding|1/1|c.397G>A|p.Val133Ile|397/663|397/663|133/220||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:790:-71.4192,-6.62266,0
Chromosome	3015140	.	C	T	980.143	.	AB=0;AO=31;DP=31;QA=1121;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv2699c-Rv2700|Rv2699c-Rv2700|intergenic_region|Rv2699c-Rv2700|||n.3015140C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1121:-101.181,-9.33193,0
Chromosome	3017276	.	A	G	715.509	.	AB=0;AO=22;DP=22;QA=821;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ppgK|Rv2702|transcript|Rv2702|protein_coding|1/1|c.419A>G|p.Asn140Ser|419/798|419/798|140/265||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:821:-74.2147,-6.62266,0
Chromosome	3027606	.	G	C	732.88	.	AB=0;AO=23;DP=23;QA=847;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv2714|Rv2714|transcript|Rv2714|protein_coding|1/1|c.542G>C|p.Trp181Ser|542/975|542/975|181/324||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:847:-76.544,-6.92369,0
Chromosome	3027798	.	C	T	710.395	.	AB=0;AO=23;DP=23;QA=818;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2714|Rv2714|transcript|Rv2714|protein_coding|1/1|c.734C>T|p.Ala245Val|734/975|734/975|245/324||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:818:-73.9275,-6.92369,0
Chromosome	3031168	.	G	A	861.043	.	AB=0;AO=28;DP=28;QA=991;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2719c|Rv2719c|transcript|Rv2719c|protein_coding|1/1|c.370C>T|p.His124Tyr|370/498|370/498|124/165||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:991:-89.495,-8.42884,0
Chromosome	3057137	.	C	T	361.374	.	AB=0;AO=13;DP=13;QA=437;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2743c|Rv2743c|transcript|Rv2743c|protein_coding|1/1|c.96G>A|p.Lys32Lys|96/813|96/813|32/270||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:437:-39.6414,-3.91339,0
Chromosome	3067901	.	G	A	633.512	.	AB=0;AO=21;DP=21;QA=748;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|thyX|Rv2754c|transcript|Rv2754c|protein_coding|1/1|c.45C>T|p.Thr15Thr|45/753|45/753|15/250||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:748:-67.6335,-6.32163,0
Chromosome	3069805	.	C	G	618.133	.	AB=0;AO=20;DP=20;QA=713;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|hsdM|Rv2756c|transcript|Rv2756c|protein_coding|1/1|c.279G>C|p.Val93Val|279/1623|279/1623|93/540||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:713:-64.4939,-6.0206,0
Chromosome	3078826	.	A	G	519.557	.	AB=0;AO=17;DP=17;QA=609;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|PE27|Rv2769c|transcript|Rv2769c|protein_coding|1/1|c.160T>C|p.Ser54Pro|160/828|160/828|54/275||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:609:-55.1352,-5.11751,0
Chromosome	3079877	.	G	A	447.634	.	AB=0;AO=16;DP=16;QA=521;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|PPE44|Rv2770c|transcript|Rv2770c|protein_coding|1/1|c.581C>T|p.Ser194Phe|581/1149|581/1149|194/382||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:521:-47.1924,-4.81648,0
Chromosome	3086208	.	G	T	840.497	.	AB=0;AO=27;DP=27;QA=967;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv2778c-Rv2779c|Rv2778c-Rv2779c|intergenic_region|Rv2778c-Rv2779c|||n.3086208G>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:967:-87.3406,-8.12781,0
Chromosome	3088625	.	G	A	784.11	.	AB=0;AO=25;DP=25;QA=913;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2781c|Rv2781c|transcript|Rv2781c|protein_coding|1/1|c.360C>T|p.Val120Val|360/1035|360/1035|120/344||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:913:-82.4817,-7.52575,0
Chromosome	3089776	.	G	A	778.654	.	AB=0;AO=27;DP=27;QA=895;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|pepR|Rv2782c|transcript|Rv2782c|protein_coding|1/1|c.586C>T|p.Arg196Trp|586/1317|586/1317|196/438||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:895:-80.8424,-8.12781,0
Chromosome	3098497	.	A	C	888.117	.	AB=0;AO=28;DP=28;QA=1021;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|fadE21|Rv2789c|transcript|Rv2789c|protein_coding|1/1|c.442T>G|p.Ser148Ala|442/1233|442/1233|148/410||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1021:-92.2023,-8.42884,0
Chromosome	3099091	.	TCCG	T	553.832	.	AB=0;AO=20;DP=20;QA=640;QR=0;RO=0;TYPE=del;ANN=T|disruptive_inframe_deletion|MODERATE|ltp1|Rv2790c|transcript|Rv2790c|protein_coding|1/1|c.1076_1078delCGG|p.Ala359del|1078/1206|1076/1206|359/401||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:640:-57.8943,-6.0206,0
Chromosome	3104189	.	G	A	1077.78	.	AB=0;AO=35;DP=35;QA=1240;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2795c|Rv2795c|transcript|Rv2795c|protein_coding|1/1|c.723C>T|p.Cys241Cys|723/975|723/975|241/324||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1240:-111.888,-10.5361,0
Chromosome	3105144	.	A	C	363.691	.	AB=0;AO=12;DP=12;QA=428;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|lppV|Rv2796c|transcript|Rv2796c|protein_coding|1/1|c.476T>G|p.Phe159Cys|476/564|476/564|159/187||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:428:-38.8513,-3.61236,0
Chromosome	3105748	.	C	T	376.52	.	AB=0;AO=14;DP=14;QA=478;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv2797c|Rv2797c|transcript|Rv2797c|protein_coding|1/1|c.1560G>A|p.Met520Ile|1560/1689|1560/1689|520/562||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:478:-43.3401,-4.21442,0
Chromosome	3112877	.	A	G	382.309	.	AB=0;AO=13;DP=13;QA=448;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2804c|Rv2804c|transcript|Rv2804c|protein_coding|1/1|c.218T>C|p.Val73Ala|218/630|218/630|73/209||,G|missense_variant|MODERATE|Rv2805|Rv2805|transcript|Rv2805|protein_coding|1/1|c.11A>G|p.Asp4Gly|11/405|11/405|4/134||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:448:-40.6424,-3.91339,0
Chromosome	3113491	.	A	AG	543.852	.	AB=0;AO=19;DP=19;QA=628;QR=0;RO=0;TYPE=ins;ANN=AG|intergenic_region|MODIFIER|Rv2806-Rv2807|Rv2806-Rv2807|intergenic_region|Rv2806-Rv2807|||n.3113491_3113492insG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:628:-56.8215,-5.71957,0
Chromosome	3114597	.	C	A	318.395	.	AB=0;AO=11;DP=11;QA=411;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2807|Rv2807|transcript|Rv2807|protein_coding|1/1|c.940C>A|p.Leu314Met|940/1155|940/1155|314/384||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:411:-37.3386,-3.31133,0
Chromosome	3118449	.	G	A	697.332	.	AB=0;AO=23;DP=23;QA=806;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2813|Rv2813|transcript|Rv2813|protein_coding|1/1|c.226G>A|p.Val76Ile|226/813|226/813|76/270||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:806:-72.843,-6.92369,0
Chromosome	3119345	.	C	T	377.306	.	AB=0;AO=14;DP=15;QA=464;QR=16;RO=1;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv2813-Rv2816c|Rv2813-Rv2816c|intergenic_region|Rv2813-Rv2816c|||n.3119345C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:15:1:16:14:464:-40.4695,-2.91547,0
Chromosome	3119513	.	T	C	510.544	.	AB=0;AO=20;DP=20;QA=615;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv2813-Rv2816c|Rv2813-Rv2816c|intergenic_region|Rv2813-Rv2816c|||n.3119513T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:615:-55.6351,-6.0206,0
Chromosome	3119737	.	GGGTT	CCGGA	287.176	.	AB=0;AO=10;DP=11;QA=347;QR=0;RO=0;TYPE=complex;ANN=CCGGA|intergenic_region|MODIFIER|Rv2813-Rv2816c|Rv2813-Rv2816c|intergenic_region|Rv2813-Rv2816c|||n.3119737_3119741delGGGTTinsCCGGA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:10:347:-31.2679,-3.0103,0
Chromosome	3122943	.	A	G	296.524	.	AB=0;AO=10;DP=10;QA=347;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv2813-Rv2816c|Rv2813-Rv2816c|intergenic_region|Rv2813-Rv2816c|||n.3122943A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:347:-31.5583,-3.0103,0
Chromosome	3122949	.	CCT	TCA	325.687	.	AB=0;AO=11;DP=11;QA=383;QR=0;RO=0;TYPE=complex;ANN=TCA|intergenic_region|MODIFIER|Rv2813-Rv2816c|Rv2813-Rv2816c|intergenic_region|Rv2813-Rv2816c|||n.3122949_3122951delCCTinsTCA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:383:-34.801,-3.31133,0
Chromosome	3129359	.	C	T	835.837	.	AB=0;AO=26;DP=26;QA=954;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2823c|Rv2823c|transcript|Rv2823c|protein_coding|1/1|c.2415G>A|p.Lys805Lys|2415/2430|2415/2430|805/809||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:954:-86.1742,-7.82678,0
Chromosome	3133054	.	GC	CG	342.541	.	AB=0;AO=12;DP=12;QA=433;QR=0;RO=0;TYPE=complex;ANN=CG|missense_variant|MODERATE|Rv2825c|Rv2825c|transcript|Rv2825c|protein_coding|1/1|c.485_486delGCinsCG|p.Cys162Ser|486/648|485/648|162/215||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:433:-38.975,-3.61236,0
Chromosome	3137237	.	C	T	409.218	.	AB=0;AO=13;DP=13;QA=475;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|vapB22-echA16|Rv2830c-Rv2831|intergenic_region|Rv2830c-Rv2831|||n.3137237C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:475:-43.0833,-3.91339,0
Chromosome	3157349	.	C	T	543.696	.	AB=0;AO=18;DP=18;QA=640;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|cobB|Rv2848c|transcript|Rv2848c|protein_coding|1/1|c.173G>A|p.Gly58Asp|173/1374|173/1374|58/457||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:640:-57.9209,-5.41854,0
Chromosome	3159998	.	CAA	C	796.146	.	AB=0;AO=30;DP=31;QA=916;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv2850c|Rv2850c|transcript|Rv2850c|protein_coding|1/1|c.55_56delTT|p.Leu19fs|56/1890|55/1890|19/629||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:30:916:-82.389,-9.0309,0
Chromosome	3170663	.	T	C	748.036	.	AB=0;AO=24;DP=24;QA=858;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|aldC|Rv2858c|transcript|Rv2858c|protein_coding|1/1|c.61A>G|p.Thr21Ala|61/1368|61/1368|21/455||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:858:-77.532,-7.22472,0
Chromosome	3174496	.	G	A	928.564	.	AB=0;AO=30;DP=30;QA=1063;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2862c|Rv2862c|transcript|Rv2862c|protein_coding|1/1|c.148C>T|p.Arg50Cys|148/585|148/585|50/194||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1063:-95.9708,-9.0309,0
Chromosome	3180988	.	A	C	396.277	.	AB=0;AO=13;DP=13;QA=462;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|rip|Rv2869c|transcript|Rv2869c|protein_coding|1/1|c.775T>G|p.Phe259Val|775/1215|775/1215|259/404||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:462:-41.9142,-3.91339,0
Chromosome	3188769	.	G	A	774.837	.	AB=0;AO=25;DP=25;QA=896;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|merT|Rv2877c|transcript|Rv2877c|protein_coding|1/1|c.103C>T|p.His35Tyr|103/864|103/864|35/287||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:896:-80.947,-7.52575,0
Chromosome	3189242	.	G	A	550.402	.	AB=0;AO=18;DP=18;QA=634;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|mpt53|Rv2878c|transcript|Rv2878c|protein_coding|1/1|c.156C>T|p.Ala52Ala|156/522|156/522|52/173||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:634:-57.3726,-5.41854,0
Chromosome	3189433	.	C	T	644.97	.	AB=0;AO=21;DP=21;QA=756;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|mpt53-cdsA|Rv2878c-Rv2881c|intergenic_region|Rv2878c-Rv2881c|||n.3189433C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:756:-68.3533,-6.32163,0
Chromosome	3189580	.	C	T	587.433	.	AB=0;AO=21;DP=21;QA=689;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|mpt53-cdsA|Rv2878c-Rv2881c|intergenic_region|Rv2878c-Rv2881c|||n.3189580C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:689:-62.3048,-6.32163,0
Chromosome	3190145	.	TC	T	330.184	.	AB=0;AO=13;DP=13;QA=389;QR=0;RO=0;TYPE=del;ANN=T|intergenic_region|MODIFIER|mpt53-cdsA|Rv2878c-Rv2881c|intergenic_region|Rv2878c-Rv2881c|||n.3190146delC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:389:-35.1799,-3.91339,0
Chromosome	3195731	.	C	T	702.335	.	AB=0;AO=25;DP=25;QA=817;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2886c|Rv2886c|transcript|Rv2886c|protein_coding|1/1|c.702G>A|p.Val234Val|702/888|702/888|234/295||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:817:-73.8173,-7.52575,0
Chromosome	3200304	.	G	A	471.463	.	AB=0;AO=16;DP=16;QA=552;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2891|Rv2891|transcript|Rv2891|protein_coding|1/1|c.39G>A|p.Val13Val|39/750|39/750|13/249||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:552:-49.9935,-4.81648,0
Chromosome	3207290	.	C	A	760.583	.	AB=0;AO=24;DP=24;QA=884;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2897c|Rv2897c|transcript|Rv2897c|protein_coding|1/1|c.653G>T|p.Gly218Val|653/1512|653/1512|218/503||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:884:-79.8788,-7.22472,0
Chromosome	3219790	.	G	A	774.113	.	AB=0;AO=25;DP=25;QA=889;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2912c|Rv2912c|transcript|Rv2912c|protein_coding|1/1|c.72C>T|p.Ile24Ile|72/588|72/588|24/195||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:889:-80.3107,-7.52575,0
Chromosome	3227488	.	A	G	519.256	.	AB=0;AO=17;DP=17;QA=610;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2917|Rv2917|transcript|Rv2917|protein_coding|1/1|c.1126A>G|p.Ser376Gly|1126/1881|1126/1881|376/626||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:610:-55.2269,-5.11751,0
Chromosome	3231091	.	C	A	852.364	.	AB=0;AO=27;DP=28;QA=988;QR=16;RO=1;TYPE=snp;ANN=A|synonymous_variant|LOW|amt|Rv2920c|transcript|Rv2920c|protein_coding|1/1|c.1416G>T|p.Val472Val|1416/1434|1416/1434|472/477||	GT:DP:RO:QR:AO:QA:GL	1/1:28:1:16:27:988:-87.6283,-6.82886,0
Chromosome	3244414	.	G	A	717.646	.	AB=0;AO=23;DP=23;QA=826;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|fadD26|Rv2930|transcript|Rv2930|protein_coding|1/1|c.718G>A|p.Val240Met|718/1752|718/1752|240/583||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:826:-74.6526,-6.92369,0
Chromosome	3247865	.	GCAAAACCGG	TAGGGACCGA	664.367	.	AB=0;AO=23;DP=23;QA=794;QR=0;RO=0;TYPE=complex;ANN=TAGGGACCGA|missense_variant|MODERATE|ppsA|Rv2931|transcript|Rv2931|protein_coding|1/1|c.2421_2430delGCAAAACCGGinsTAGGGACCGA|p.GlnAsn808ArgAsp|2421/5631|2421/5631|807/1876||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:794:-71.7701,-6.92369,0
Chromosome	3249411	.	G	A	697.222	.	AB=0;AO=22;DP=22;QA=805;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ppsA|Rv2931|transcript|Rv2931|protein_coding|1/1|c.3967G>A|p.Gly1323Ser|3967/5631|3967/5631|1323/1876||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:805:-72.7699,-6.62266,0
Chromosome	3251956	.	C	G	876.505	.	AB=0;AO=29;DP=29;QA=1019;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|ppsB|Rv2932|transcript|Rv2932|protein_coding|1/1|c.885C>G|p.Arg295Arg|885/4617|885/4617|295/1538||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1019:-92.0162,-8.72987,0
Chromosome	3254880	.	T	G	769.995	.	AB=0;AO=24;DP=24;QA=887;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ppsB|Rv2932|transcript|Rv2932|protein_coding|1/1|c.3809T>G|p.Leu1270Arg|3809/4617|3809/4617|1270/1538||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:887:-80.1483,-7.22472,0
Chromosome	3258274	.	A	C	338.653	.	AB=0;AO=12;DP=12;QA=410;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ppsC|Rv2933|transcript|Rv2933|protein_coding|1/1|c.2590A>C|p.Ser864Arg|2590/6567|2590/6567|864/2188||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:410:-37.2226,-3.61236,0
Chromosome	3266030	.	G	A	748.068	.	AB=0;AO=26;DP=26;QA=926;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ppsD|Rv2934|transcript|Rv2934|protein_coding|1/1|c.3783G>A|p.Ser1261Ser|3783/5484|3783/5484|1261/1827||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:926:-83.6522,-7.82678,0
Chromosome	3266288	.	C	G	564.832	.	AB=0;AO=18;DP=18;QA=654;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|ppsD|Rv2934|transcript|Rv2934|protein_coding|1/1|c.4041C>G|p.Ser1347Ser|4041/5484|4041/5484|1347/1827||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:654:-59.188,-5.41854,0
Chromosome	3271037	.	G	A	898.67	.	AB=0;AO=29;DP=29;QA=1031;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ppsE|Rv2935|transcript|Rv2935|protein_coding|1/1|c.3301G>A|p.Asp1101Asn|3301/4467|3301/4467|1101/1488||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1031:-93.0873,-8.72987,0
Chromosome	3273138	.	G	C	992.95	.	AB=0;AO=32;DP=32;QA=1135;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|drrA|Rv2936|transcript|Rv2936|protein_coding|1/1|c.925G>C|p.Asp309His|925/996|925/996|309/331||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1135:-102.439,-9.63296,0
Chromosome	3289923	.	C	A	649.66	.	AB=0;AO=21;DP=21;QA=754;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2944|Rv2944|transcript|Rv2944|protein_coding|1/1|c.134C>A|p.Pro45His|134/717|134/717|45/238||,A|synonymous_variant|LOW|Rv2943A|Rv2943A|transcript|Rv2943A|protein_coding|1/1|c.219C>A|p.Ala73Ala|219/531|219/531|73/176||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:754:-68.1807,-6.32163,0
Chromosome	3296721	.	G	C	444.513	.	AB=0;AO=14;DP=14;QA=516;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|pks15|Rv2947c|transcript|Rv2947c|protein_coding|1/1|c.1120C>G|p.Arg374Gly|1120/1491|1120/1491|374/496||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:516:-46.78,-4.21442,0
Chromosome	3302683	.	T	C	825.223	.	AB=0;AO=26;DP=26;QA=948;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|fadD29-Rv2951c|Rv2950c-Rv2951c|intergenic_region|Rv2950c-Rv2951c|||n.3302683T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:948:-85.635,-7.82678,0
Chromosome	3303669	.	C	A	905.126	.	AB=0;AO=29;DP=29;QA=1033;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2951c|Rv2951c|transcript|Rv2951c|protein_coding|1/1|c.580G>T|p.Ala194Ser|580/1146|580/1146|194/381||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1033:-93.2658,-8.72987,0
Chromosome	3308489	.	C	T	817.228	.	AB=0;AO=27;DP=27;QA=935;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2955c|Rv2955c|transcript|Rv2955c|protein_coding|1/1|c.57G>A|p.Pro19Pro|57/966|57/966|19/321||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:935:-84.4486,-8.12781,0
Chromosome	3311119	.	C	G	286.591	.	AB=0;AO=10;DP=10;QA=355;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv2958c|Rv2958c|transcript|Rv2958c|protein_coding|1/1|c.882G>C|p.Val294Val|882/1287|882/1287|294/428||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:355:-32.2886,-3.0103,0
Chromosome	3314412	.	G	A	745.1	.	AB=0;AO=24;DP=24;QA=861;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2962c|Rv2962c|transcript|Rv2962c|protein_coding|1/1|c.711C>T|p.Ala237Ala|711/1350|711/1350|237/449||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:861:-77.8039,-7.22472,0
Chromosome	3326554	.	C	A	819.966	.	AB=0;AO=29;DP=29;QA=965;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv2971|Rv2971|transcript|Rv2971|protein_coding|1/1|c.454C>A|p.His152Asn|454/849|454/849|152/282||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:965:-87.1388,-8.72987,0
Chromosome	3335708	.	C	G	482.694	.	AB=0;AO=15;DP=15;QA=561;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2979c|Rv2979c|transcript|Rv2979c|protein_coding|1/1|c.41G>C|p.Arg14Pro|41/585|41/585|14/194||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:561:-50.8303,-4.51545,0
Chromosome	3352244	.	A	G	954.967	.	AB=0;AO=30;DP=30;QA=1091;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv2994|Rv2994|transcript|Rv2994|protein_coding|1/1|c.976A>G|p.Thr326Ala|976/1338|976/1338|326/445||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1091:-98.4958,-9.0309,0
Chromosome	3363866	.	G	A	1150.3	.	AB=0;AO=38;DP=38;QA=1313;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3005c|Rv3005c|transcript|Rv3005c|protein_coding|1/1|c.667C>T|p.Leu223Leu|667/840|667/840|223/279||	GT:DP:RO:QR:AO:QA:GL	1/1:38:0:0:38:1313:-118.443,-11.4391,0
Chromosome	3369869	.	T	G	638.339	.	AB=0;AO=20;DP=20;QA=752;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|pfkA-gatA|Rv3010c-Rv3011c|intergenic_region|Rv3010c-Rv3011c|||n.3369869T>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:752:-68.0099,-6.0206,0
Chromosome	3371260	.	C	T	435.657	.	AB=0;AO=15;DP=15;QA=509;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|gatA|Rv3011c|transcript|Rv3011c|protein_coding|1/1|c.175G>A|p.Val59Ile|175/1485|175/1485|59/494||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:509:-46.1266,-4.51545,0
Chromosome	3415332	.	G	A	443.217	.	AB=0;AO=14;DP=14;QA=512;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|nrdH-Rv3054c|Rv3053c-Rv3054c|intergenic_region|Rv3053c-Rv3054c|||n.3415332G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:512:-46.4163,-4.21442,0
Chromosome	3420388	.	C	T	832.497	.	AB=0;AO=28;DP=28;QA=954;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|cyp136|Rv3059|transcript|Rv3059|protein_coding|1/1|c.897C>T|p.Phe299Phe|897/1479|897/1479|299/492||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:954:-86.1478,-8.42884,0
Chromosome	3420825	.	G	A	775.3	.	AB=0;AO=26;DP=26;QA=887;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|cyp136|Rv3059|transcript|Rv3059|protein_coding|1/1|c.1334G>A|p.Gly445Asp|1334/1479|1334/1479|445/492||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:887:-80.1205,-7.82678,0
Chromosome	3428374	.	C	G	663.318	.	AB=0;AO=21;DP=21;QA=761;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|cstA|Rv3063|transcript|Rv3063|protein_coding|1/1|c.1132C>G|p.His378Asp|1132/2277|1132/2277|378/758||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:761:-68.8128,-6.32163,0
Chromosome	3435765	.	G	T	709.38	.	AB=0;AO=25;DP=25;QA=829;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv3071-Rv3072c|Rv3071-Rv3072c|intergenic_region|Rv3071-Rv3072c|||n.3435765G>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:829:-74.902,-7.52575,0
Chromosome	3440542	.	G	A	769.53	.	AB=0;AO=24;DP=24;QA=892;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|atsF|Rv3077|transcript|Rv3077|protein_coding|1/1|c.1002G>A|p.Gly334Gly|1002/1812|1002/1812|334/603||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:892:-80.6015,-7.22472,0
Chromosome	3440895	.	G	A	654.436	.	AB=0;AO=22;DP=22;QA=755;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|atsF|Rv3077|transcript|Rv3077|protein_coding|1/1|c.1355G>A|p.Arg452His|1355/1812|1355/1812|452/603||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:755:-68.2616,-6.62266,0
Chromosome	3442631	.	G	T	976.765	.	AB=0;AO=30;DP=30;QA=1132;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|Rv3079c-pknK|Rv3079c-Rv3080c|intergenic_region|Rv3079c-Rv3080c|||n.3442631G>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1132:-102.186,-9.0309,0
Chromosome	3454263	.	G	C	1198.67	.	AB=0;AO=37;DP=37;QA=1365;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3087|Rv3087|transcript|Rv3087|protein_coding|1/1|c.1339G>C|p.Val447Leu|1339/1419|1339/1419|447/472||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1365:-123.138,-11.1381,0
Chromosome	3457514	.	C	G	840.602	.	AB=0;AO=28;DP=28;QA=998;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|fadD13-Rv3090|Rv3089-Rv3090|intergenic_region|Rv3089-Rv3090|||n.3457514C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:998:-90.1302,-8.42884,0
Chromosome	3458659	.	G	A	820.641	.	AB=0;AO=26;DP=26;QA=943;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3090|Rv3090|transcript|Rv3090|protein_coding|1/1|c.449G>A|p.Arg150His|449/888|449/888|150/295||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:943:-85.1768,-7.82678,0
Chromosome	3464629	.	G	A	634.285	.	AB=0;AO=20;DP=20;QA=730;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3096|Rv3096|transcript|Rv3096|protein_coding|1/1|c.83G>A|p.Gly28Glu|83/1140|83/1140|28/379||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:730:-66.0231,-6.0206,0
Chromosome	3465812	.	G	A	985.443	.	AB=0;AO=30;DP=30;QA=1123;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lipY|Rv3097c|transcript|Rv3097c|protein_coding|1/1|c.1280C>T|p.Pro427Leu|1280/1314|1280/1314|427/437||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1123:-101.375,-9.0309,0
Chromosome	3466919	.	G	C	411.856	.	AB=0;AO=14;DP=14;QA=480;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|lipY|Rv3097c|transcript|Rv3097c|protein_coding|1/1|c.173C>G|p.Ala58Gly|173/1314|173/1314|58/437||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:480:-43.5143,-4.21442,0
Chromosome	3467465	.	G	C	1017.72	.	AB=0;AO=32;DP=32;QA=1172;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv3098c|Rv3098c|transcript|Rv3098c|protein_coding|1/1|c.198C>G|p.Ala66Ala|198/453|198/453|66/150||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1172:-105.776,-9.63296,0
Chromosome	3473996	.	G	GA	508.636	.	AB=0;AO=18;DP=18;QA=596;QR=0;RO=0;TYPE=ins;ANN=GA|intergenic_region|MODIFIER|prfB-fprA|Rv3105c-Rv3106|intergenic_region|Rv3105c-Rv3106|||n.3473996_3473997insA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:596:-53.9408,-5.41854,0
Chromosome	3475159	.	G	A	377.778	.	AB=0;AO=12;DP=12;QA=442;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|fprA|Rv3106|transcript|Rv3106|protein_coding|1/1|c.1153G>A|p.Asp385Asn|1153/1371|1153/1371|385/456||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:442:-40.1229,-3.61236,0
Chromosome	3480722	.	G	A	893.263	.	AB=0;AO=28;DP=28;QA=1020;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3113|Rv3113|transcript|Rv3113|protein_coding|1/1|c.649G>A|p.Ala217Thr|649/669|649/669|217/222||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1020:-92.1043,-8.42884,0
Chromosome	3480789	.	C	T	857.43	.	AB=0;AO=26;DP=26;QA=978;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3114|Rv3114|transcript|Rv3114|protein_coding|1/1|c.31C>T|p.Pro11Ser|31/531|31/531|11/176||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:978:-88.3335,-7.82678,0
Chromosome	3498418	.	G	A	301.943	.	AB=0;AO=10;DP=10;QA=353;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|devS|Rv3132c|transcript|Rv3132c|protein_coding|1/1|c.848C>T|p.Thr283Ile|848/1737|848/1737|283/578||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:353:-32.1001,-3.0103,0
Chromosome	3505005	.	C	A	493.609	.	AB=0;AO=18;DP=18;QA=588;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|pflA|Rv3138|transcript|Rv3138|protein_coding|1/1|c.811C>A|p.Pro271Thr|811/1089|811/1089|271/362||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:588:-53.2211,-5.41854,0
Chromosome	3509091	.	C	G	1135.39	.	AB=0;AO=37;DP=37;QA=1307;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|fadB4-Rv3142c|Rv3141-Rv3142c|intergenic_region|Rv3141-Rv3142c|||n.3509091C>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1307:-117.916,-11.1381,0
Chromosome	3510120	.	G	T	635.015	.	AB=0;AO=20;DP=20;QA=729;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE52|Rv3144c|transcript|Rv3144c|protein_coding|1/1|c.1198C>A|p.Gln400Lys|1198/1230|1198/1230|400/409||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:729:-65.9298,-6.0206,0
Chromosome	3517548	.	A	G	437.442	.	AB=0;AO=15;DP=15;QA=516;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|nuoG|Rv3151|transcript|Rv3151|protein_coding|1/1|c.803A>G|p.Glu268Gly|803/2421|803/2421|268/806||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:516:-46.7566,-4.51545,0
Chromosome	3521044	.	G	A	883.398	.	AB=0;AO=29;DP=29;QA=1014;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|nuoI|Rv3153|transcript|Rv3153|protein_coding|1/1|c.538G>A|p.Ala180Thr|538/636|538/636|180/211||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1014:-91.5617,-8.72987,0
Chromosome	3530955	.	G	C	854.001	.	AB=0;AO=27;DP=27;QA=980;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3161c|Rv3161c|transcript|Rv3161c|protein_coding|1/1|c.184C>G|p.Leu62Val|184/1149|184/1149|62/382||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:980:-88.5081,-8.12781,0
Chromosome	3544710	.	T	C	436.73	.	AB=0;AO=14;DP=14;QA=510;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|mesT|Rv3176c|transcript|Rv3176c|protein_coding|1/1|c.591A>G|p.Pro197Pro|591/957|591/957|197/318||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:510:-46.2358,-4.21442,0
Chromosome	3555699	.	G	A	667.812	.	AB=0;AO=21;DP=21;QA=778;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3190c|Rv3190c|transcript|Rv3190c|protein_coding|1/1|c.989C>T|p.Ala330Val|989/1266|989/1266|330/421||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:778:-70.3427,-6.32163,0
Chromosome	3556607	.	G	T	505.899	.	AB=0;AO=16;DP=16;QA=582;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3190c|Rv3190c|transcript|Rv3190c|protein_coding|1/1|c.81C>A|p.Ser27Arg|81/1266|81/1266|27/421||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:582:-52.7106,-4.81648,0
Chromosome	3560645	.	T	C	685.374	.	AB=0;AO=23;DP=23;QA=801;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3193c|Rv3193c|transcript|Rv3193c|protein_coding|1/1|c.2528A>G|p.Gln843Arg|2528/2979|2528/2979|843/992||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:801:-72.3986,-6.92369,0
Chromosome	3566943	.	G	A	510.664	.	AB=0;AO=16;DP=17;QA=597;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv3196A-Rv3197|Rv3196A-Rv3197|intergenic_region|Rv3196A-Rv3197|||n.3566943G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:16:597:-53.9136,-4.81648,0
Chromosome	3567600	.	G	A	899.256	.	AB=0;AO=29;DP=29;QA=1051;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3197|Rv3197|transcript|Rv3197|protein_coding|1/1|c.577G>A|p.Val193Met|577/1344|577/1344|193/447||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1051:-94.8917,-8.72987,0
Chromosome	3571834	.	G	T	378.222	.	AB=0;AO=12;DP=12;QA=441;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|nudC|Rv3199c|transcript|Rv3199c|protein_coding|1/1|c.710C>A|p.Pro237Gln|710/942|710/942|237/313||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:441:-40.0333,-3.61236,0
Chromosome	3573636	.	C	T	506.218	.	AB=0;AO=16;DP=16;QA=594;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3200c|Rv3200c|transcript|Rv3200c|protein_coding|1/1|c.34G>A|p.Asp12Asn|34/1068|34/1068|12/355||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:594:-53.7981,-4.81648,0
Chromosome	3580636	.	CT	C	804.008	.	AB=0;AO=27;DP=28;QA=924;QR=0;RO=0;TYPE=del;ANN=C|intergenic_region|MODIFIER|Rv3202a-lipV|Rv3202a-Rv3203|intergenic_region|Rv3202a-Rv3203|||n.3580637delT||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:27:924:-83.3156,-8.12781,0
Chromosome	3583295	.	C	T	1000.51	.	AB=0;AO=32;DP=32;QA=1141;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|moeB1|Rv3206c|transcript|Rv3206c|protein_coding|1/1|c.416G>A|p.Gly139Asp|416/1179|416/1179|139/392||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1141:-102.983,-9.63296,0
Chromosome	3590686	.	G	GC	434.033	.	AB=0;AO=14;DP=14;QA=507;QR=0;RO=0;TYPE=ins;ANN=GC|intergenic_region|MODIFIER|Rv3212-Rv3213c|Rv3212-Rv3213c|intergenic_region|Rv3212-Rv3213c|||n.3590686_3590687insC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:507:-45.9661,-4.21442,0
Chromosome	3595036	.	C	T	810.354	.	AB=0;AO=26;DP=26;QA=928;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3218|Rv3218|transcript|Rv3218|protein_coding|1/1|c.569C>T|p.Pro190Leu|569/966|569/966|190/321||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:928:-83.8207,-7.82678,0
Chromosome	3597737	.	C	T	877.426	.	AB=0;AO=27;DP=27;QA=1006;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|TB7.3|Rv3221c|transcript|Rv3221c|protein_coding|1/1|c.30G>A|p.Val10Val|30/216|30/216|10/71||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:1006:-90.8446,-8.12781,0
Chromosome	3603355	.	G	A	716.591	.	AB=0;AO=23;DP=23;QA=824;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv3226c-aroA|Rv3226c-Rv3227|intergenic_region|Rv3226c-Rv3227|||n.3603355G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:824:-74.4746,-6.92369,0
Chromosome	3621044	.	T	C	563.212	.	AB=0;AO=18;DP=18;QA=665;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3241c|Rv3241c|transcript|Rv3241c|protein_coding|1/1|c.211A>G|p.Ile71Val|211/645|211/645|71/214||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:665:-60.1814,-5.41854,0
Chromosome	3624486	.	C	T	766.537	.	AB=0;AO=24;DP=24;QA=884;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|lpqB|Rv3244c|transcript|Rv3244c|protein_coding|1/1|c.425G>A|p.Gly142Asp|425/1752|425/1752|142/583||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:884:-79.8763,-7.22472,0
Chromosome	3629928	.	T	C	848.54	.	AB=0;AO=27;DP=27;QA=984;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3249c|Rv3249c|transcript|Rv3249c|protein_coding|1/1|c.460A>G|p.Thr154Ala|460/636|460/636|154/211||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:984:-88.8715,-8.12781,0
Chromosome	3638093	.	A	G	431.274	.	AB=0;AO=15;DP=15;QA=526;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|pmmA|Rv3257c|transcript|Rv3257c|protein_coding|1/1|c.617T>C|p.Leu206Ser|617/1398|617/1398|206/465||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:526:-47.6584,-4.51545,0
Chromosome	3647041	.	G	A	577.408	.	AB=0;AO=19;DP=19;QA=677;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|rmlD|Rv3266c|transcript|Rv3266c|protein_coding|1/1|c.769C>T|p.Pro257Ser|769/915|769/915|257/304||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:677:-61.2532,-5.71957,0
Chromosome	3649543	.	G	A	661.252	.	AB=0;AO=22;DP=22;QA=775;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3268|Rv3268|transcript|Rv3268|protein_coding|1/1|c.124G>A|p.Asp42Asn|124/690|124/690|42/229||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:775:-70.0653,-6.62266,0
Chromosome	3658266	.	G	C	331.798	.	AB=0;AO=11;DP=11;QA=398;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|purE|Rv3275c|transcript|Rv3275c|protein_coding|1/1|c.373C>G|p.Arg125Gly|373/525|373/525|125/174||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:398:-36.1603,-3.31133,0
Chromosome	3670040	.	T	C	535.0	.	AB=0;AO=17;DP=17;QA=625;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv3289c|Rv3289c|transcript|Rv3289c|protein_coding|1/1|c.372A>G|p.Ala124Ala|372/378|372/378|124/125||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:625:-56.5826,-5.11751,0
Chromosome	3678813	.	T	A	730.23	.	AB=0;AO=26;DP=26;QA=850;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lhr|Rv3296|transcript|Rv3296|protein_coding|1/1|c.2039T>A|p.Ile680Asn|2039/4542|2039/4542|680/1513||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:850:-76.7885,-7.82678,0
Chromosome	3679949	.	G	A	493.151	.	AB=0;AO=16;DP=16;QA=569;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lhr|Rv3296|transcript|Rv3296|protein_coding|1/1|c.3175G>A|p.Glu1059Lys|3175/4542|3175/4542|1059/1513||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:569:-51.5381,-4.81648,0
Chromosome	3681548	.	C	A	854.795	.	AB=0;AO=27;DP=27;QA=978;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|nei|Rv3297|transcript|Rv3297|protein_coding|1/1|c.229C>A|p.Arg77Arg|229/768|229/768|77/255||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:978:-88.3322,-8.12781,0
Chromosome	3683037	.	C	T	1056.24	.	AB=0;AO=37;DP=37;QA=1208;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|lpqC-atsB|Rv3298c-Rv3299c|intergenic_region|Rv3298c-Rv3299c|||n.3683037C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1208:-108.986,-11.1381,0
Chromosome	3690016	.	G	A	588.57	.	AB=0;AO=19;DP=20;QA=688;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lpdA|Rv3303c|transcript|Rv3303c|protein_coding|1/1|c.923C>T|p.Ser308Leu|923/1482|923/1482|308/493||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:19:688:-62.1062,-5.71957,0
Chromosome	3692357	.	G	C	876.163	.	AB=0;AO=28;DP=28;QA=1001;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|amiA1|Rv3305c|transcript|Rv3305c|protein_coding|1/1|c.452C>G|p.Ala151Gly|452/1170|452/1170|151/389||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1001:-90.3942,-8.42884,0
Chromosome	3693681	.	C	A	585.443	.	AB=0;AO=19;DP=19;QA=674;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|amiB1|Rv3306c|transcript|Rv3306c|protein_coding|1/1|c.309G>T|p.Ala103Ala|309/1185|309/1185|103/394||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:674:-60.9806,-5.71957,0
Chromosome	3696181	.	G	A	352.341	.	AB=0;AO=13;DP=13;QA=427;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|pmmB|Rv3308|transcript|Rv3308|protein_coding|1/1|c.1318G>A|p.Gly440Ser|1318/1605|1318/1605|440/534||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:427:-38.7381,-3.91339,0
Chromosome	3697708	.	G	A	552.967	.	AB=0;AO=19;DP=19;QA=644;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|sapM|Rv3310|transcript|Rv3310|protein_coding|1/1|c.511G>A|p.Ala171Thr|511/900|511/900|171/299||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:644:-58.265,-5.71957,0
Chromosome	3709949	.	G	A	489.606	.	AB=0;AO=16;DP=16;QA=564;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|moaC3|Rv3324c|transcript|Rv3324c|protein_coding|1/1|c.300C>T|p.Leu100Leu|300/534|300/534|100/177||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:564:-51.0813,-4.81648,0
Chromosome	3714108	.	G	A	428.461	.	AB=0;AO=16;DP=17;QA=518;QR=18;RO=1;TYPE=snp;ANN=A|synonymous_variant|LOW|sigJ|Rv3328c|transcript|Rv3328c|protein_coding|1/1|c.225C>T|p.Thr75Thr|225/939|225/939|75/312||	GT:DP:RO:QR:AO:QA:GL	1/1:17:1:18:16:518:-45.1193,-3.31754,0
Chromosome	3717562	.	C	CGGT	649.741	.	AB=0;AO=22;DP=23;QA=750;QR=0;RO=0;TYPE=ins;ANN=CGGT|conservative_inframe_insertion|MODERATE|sugI|Rv3331|transcript|Rv3331|protein_coding|1/1|c.484_486dupGTG|p.Val162dup|487/1509|487/1509|163/502||INFO_REALIGN_3_PRIME	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:22:750:-67.4862,-6.62266,0
Chromosome	3727746	.	G	A	412.657	.	AB=0;AO=14;DP=15;QA=487;QR=17;RO=1;TYPE=snp;ANN=A|missense_variant|MODERATE|metA|Rv3341|transcript|Rv3341|protein_coding|1/1|c.259G>A|p.Gly87Ser|259/1140|259/1140|87/379||	GT:DP:RO:QR:AO:QA:GL	1/1:15:1:17:14:487:-42.4572,-2.81547,0
Chromosome	3743549	.	G	A	703.541	.	AB=0;AO=24;DP=24;QA=815;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv3346c-PPE55|Rv3346c-Rv3347c|intergenic_region|Rv3346c-Rv3347c|||n.3743549G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:815:-73.648,-7.22472,0
Chromosome	3744452	.	A	C	637.608	.	AB=0;AO=21;DP=21;QA=737;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.8733T>G|p.Pro2911Pro|8733/9474|8733/9474|2911/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:737:-66.6446,-6.32163,0
Chromosome	3746845	.	C	T	548.582	.	AB=0;AO=18;DP=18;QA=635;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.6340G>A|p.Val2114Ile|6340/9474|6340/9474|2114/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:635:-57.4672,-5.41854,0
Chromosome	3750177	.	TC	AA	801.02	.	AB=0;AO=25;DP=25;QA=918;QR=0;RO=0;TYPE=complex;ANN=AA|missense_variant|MODERATE|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.3007_3008delGAinsTT|p.Asp1003Phe|3008/9474|3007/9474|1003/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:918:-82.9345,-7.52575,0
Chromosome	3750185	.	G	C	778.58	.	AB=0;AO=24;DP=24;QA=895;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.3000C>G|p.Ser1000Ser|3000/9474|3000/9474|1000/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:895:-80.8673,-7.22472,0
Chromosome	3750205	.	TGACGG	CGACAT	620.447	.	AB=0;AO=20;DP=20;QA=727;QR=0;RO=0;TYPE=complex;ANN=CGACAT|missense_variant|MODERATE|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.2975_2980delCCGTCAinsATGTCG|p.ThrValAsn992AsnValAsp|2980/9474|2975/9474|992/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:727:-65.4243,-6.0206,0
Chromosome	3750407	.	C	G	438.826	.	AB=0;AO=14;DP=14;QA=515;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.2778G>C|p.Gly926Gly|2778/9474|2778/9474|926/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:515:-46.6884,-4.21442,0
Chromosome	3750417	.	TAGCC	AAGCT	390.883	.	AB=0;AO=13;DP=13;QA=476;QR=0;RO=0;TYPE=complex;ANN=AAGCT|missense_variant|MODERATE|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.2764_2768delGGCTAinsAGCTT|p.GlyTyr922SerPhe|2768/9474|2764/9474|922/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:476:-42.8475,-3.91339,0
Chromosome	3752809	.	GCAGG	ACAGA	329.248	.	AB=0;AO=11;DP=11;QA=394;QR=0;RO=0;TYPE=complex;ANN=ACAGA|synonymous_variant|LOW|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.372_376delCCTGCinsTCTGT|p.127|376/9474|372/9474|124/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:394:-35.4581,-3.31133,0
Chromosome	3752821	.	T	C	339.969	.	AB=0;AO=11;DP=11;QA=407;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|PPE55|Rv3347c|transcript|Rv3347c|protein_coding|1/1|c.364A>G|p.Met122Val|364/9474|364/9474|122/3157||	GT:DP:RO:QR:AO:QA:GL	1/1:11:0:0:11:407:-36.9774,-3.31133,0
Chromosome	3757052	.	T	C	733.413	.	AB=0;AO=23;DP=23;QA=841;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|PPE56|Rv3350c|transcript|Rv3350c|protein_coding|1/1|c.10051A>G|p.Thr3351Ala|10051/11151|10051/11151|3351/3716||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:841:-76.0106,-6.92369,0
Chromosome	3771628	.	C	A	373.935	.	AB=0;AO=13;DP=13;QA=436;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3359|Rv3359|transcript|Rv3359|protein_coding|1/1|c.285C>A|p.Ile95Ile|285/1191|285/1191|95/396||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:436:-39.5551,-3.91339,0
Chromosome	3772616	.	A	G	691.712	.	AB=0;AO=22;DP=22;QA=793;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv3359-Rv3360|Rv3359-Rv3360|intergenic_region|Rv3359-Rv3360|||n.3772616A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:793:-71.6833,-6.62266,0
Chromosome	3783058	.	G	A	758.308	.	AB=0;AO=25;DP=25;QA=890;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|dnaE2|Rv3370c|transcript|Rv3370c|protein_coding|1/1|c.1683C>T|p.Ser561Ser|1683/3240|1683/3240|561/1079||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:890:-80.4097,-7.52575,0
Chromosome	3785946	.	G	A	727.556	.	AB=0;AO=23;DP=23;QA=837;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3371|Rv3371|transcript|Rv3371|protein_coding|1/1|c.1015G>A|p.Gly339Arg|1015/1341|1015/1341|339/446||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:837:-75.6436,-6.92369,0
Chromosome	3786033	.	G	A	529.05	.	AB=0;AO=17;DP=17;QA=623;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3371|Rv3371|transcript|Rv3371|protein_coding|1/1|c.1102G>A|p.Val368Ile|1102/1341|1102/1341|368/446||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:623:-56.4026,-5.11751,0
Chromosome	3786162	.	G	T	641.513	.	AB=0;AO=21;DP=21;QA=744;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3371|Rv3371|transcript|Rv3371|protein_coding|1/1|c.1231G>T|p.Asp411Tyr|1231/1341|1231/1341|411/446||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:744:-67.2739,-6.32163,0
Chromosome	3788365	.	G	T	560.939	.	AB=0;AO=17;DP=17;QA=645;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained&splice_region_variant|HIGH|echA18|Rv3373|transcript|Rv3373|protein_coding|1/1|c.640G>T|p.Gly214*|640/642|640/642|214/213||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:645:-58.386,-5.11751,0
Chromosome	3791438	.	T	C	966.884	.	AB=0;AO=31;DP=31;QA=1116;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3377c|Rv3377c|transcript|Rv3377c|protein_coding|1/1|c.916A>G|p.Lys306Glu|916/1506|916/1506|306/501||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1116:-100.738,-9.33193,0
Chromosome	3798451	.	C	G	890.215	.	AB=0;AO=28;DP=28;QA=1020;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|idsB|Rv3383c|transcript|Rv3383c|protein_coding|1/1|c.39G>C|p.Gly13Gly|39/1053|39/1053|13/350||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1020:-92.1035,-8.42884,0
Chromosome	3805526	.	T	G	673.968	.	AB=0;AO=22;DP=22;QA=800;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|lpqD|Rv3390|transcript|Rv3390|protein_coding|1/1|c.662T>G|p.Val221Gly|662/711|662/711|221/236||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:800:-72.3203,-6.62266,0
Chromosome	3808103	.	C	T	856.631	.	AB=0;AO=28;DP=28;QA=978;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|cmaA1|Rv3392c|transcript|Rv3392c|protein_coding|1/1|c.335G>A|p.Ser112Asn|335/864|335/864|112/287||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:978:-88.3197,-8.42884,0
Chromosome	3811629	.	A	G	507.448	.	AB=0;AO=17;DP=17;QA=588;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3395c|Rv3395c|transcript|Rv3395c|protein_coding|1/1|c.8T>C|p.Val3Ala|8/615|8/615|3/204||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:588:-53.2331,-5.11751,0
Chromosome	3812821	.	A	C	633.453	.	AB=0;AO=20;DP=20;QA=730;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|guaA|Rv3396c|transcript|Rv3396c|protein_coding|1/1|c.1258T>G|p.Leu420Val|1258/1578|1258/1578|420/525||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:730:-66.0259,-6.0206,0
Chromosome	3830695	.	G	A	541.862	.	AB=0;AO=17;DP=17;QA=626;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|guaB2|Rv3411c|transcript|Rv3411c|protein_coding|1/1|c.825C>T|p.Ala275Ala|825/1590|825/1590|275/529||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:626:-56.6745,-5.11751,0
Chromosome	3851888	.	C	T	473.363	.	AB=0;AO=16;DP=16;QA=554;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3433c|Rv3433c|transcript|Rv3433c|protein_coding|1/1|c.1326G>A|p.Ala442Ala|1326/1422|1326/1422|442/473||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:554:-50.1835,-4.81648,0
Chromosome	3854174	.	G	A	860.288	.	AB=0;AO=27;DP=27;QA=982;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3435c|Rv3435c|transcript|Rv3435c|protein_coding|1/1|c.620C>T|p.Ala207Val|620/855|620/855|207/284||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:982:-88.6917,-8.12781,0
Chromosome	3862472	.	GA	G	484.392	.	AB=0;AO=18;DP=18;QA=605;QR=0;RO=0;TYPE=del;ANN=G|intergenic_region|MODIFIER|rplM-esxT|Rv3443c-Rv3444c|intergenic_region|Rv3443c-Rv3444c|||n.3862473delA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:605:-54.7557,-5.41854,0
Chromosome	3863814	.	C	A	914.227	.	AB=0;AO=30;DP=30;QA=1063;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3446c|Rv3446c|transcript|Rv3446c|protein_coding|1/1|c.718G>T|p.Gly240Cys|718/1215|718/1215|240/404||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1063:-95.9657,-9.0309,0
Chromosome	3866350	.	C	T	867.478	.	AB=0;AO=28;DP=28;QA=992;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|eccC4|Rv3447c|transcript|Rv3447c|protein_coding|1/1|c.1889G>A|p.Gly630Glu|1889/3711|1889/3711|630/1236||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:992:-89.5848,-8.42884,0
Chromosome	3871246	.	C	T	715.37	.	AB=0;AO=24;DP=24;QA=821;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|eccB4|Rv3450c|transcript|Rv3450c|protein_coding|1/1|c.1251G>A|p.Gly417Gly|1251/1413|1251/1413|417/470||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:821:-74.194,-7.22472,0
Chromosome	3872726	.	C	T	715.696	.	AB=0;AO=25;DP=25;QA=822;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|cut3|Rv3451|transcript|Rv3451|protein_coding|1/1|c.110C>T|p.Pro37Leu|110/789|110/789|37/262||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:822:-74.2674,-7.52575,0
Chromosome	3873242	.	G	A	839.313	.	AB=0;AO=27;DP=28;QA=996;QR=37;RO=1;TYPE=snp;ANN=A|missense_variant|MODERATE|cut3|Rv3451|transcript|Rv3451|protein_coding|1/1|c.626G>A|p.Gly209Asp|626/789|626/789|209/262||	GT:DP:RO:QR:AO:QA:GL	1/1:28:1:37:27:996:-86.2551,-4.73101,0
Chromosome	3874725	.	TC	A	776.614	.	AB=0;AO=24;DP=24;QA=902;QR=0;RO=0;TYPE=complex;ANN=A|intragenic_variant|MODIFIER|Rv3453|Rv3453|gene_variant|Rv3453|||n.3874725_3874726delTCinsA||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:902:-81.2361,-7.22472,0
Chromosome	3876910	.	C	T	618.867	.	AB=0;AO=20;DP=20;QA=712;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|rplQ|Rv3456c|transcript|Rv3456c|protein_coding|1/1|c.523G>A|p.Ala175Thr|523/543|523/543|175/180||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:712:-64.3979,-6.0206,0
Chromosome	3887921	.	A	G	669.204	.	AB=0;AO=23;DP=24;QA=795;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|ilvB2|Rv3470c|transcript|Rv3470c|protein_coding|1/1|c.882T>C|p.Phe294Phe|882/1659|882/1659|294/552||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:23:795:-71.4823,-6.92369,0
Chromosome	3890310	.	G	A	462.328	.	AB=0;AO=15;DP=15;QA=536;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|bpoA|Rv3473c|transcript|Rv3473c|protein_coding|1/1|c.424C>T|p.Arg142Trp|424/786|424/786|142/261||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:536:-48.5718,-4.51545,0
Chromosome	3893480	.	A	G	798.274	.	AB=0;AO=25;DP=25;QA=915;QR=0;RO=0;TYPE=snp;ANN=G|intragenic_variant|MODIFIER|kgtP|Rv3476c|gene_variant|Rv3476c|||n.3893480A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:915:-82.6599,-7.52575,0
Chromosome	3895055	.	A	G	1043.31	.	AB=0;AO=33;DP=33;QA=1190;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|PPE60|Rv3478|transcript|Rv3478|protein_coding|1/1|c.630A>G|p.Gln210Gln|630/1182|630/1182|210/393||	GT:DP:RO:QR:AO:QA:GL	1/1:33:0:0:33:1190:-107.394,-9.93399,0
Chromosome	3895269	.	G	C	462.747	.	AB=0;AO=15;DP=15;QA=548;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|PPE60|Rv3478|transcript|Rv3478|protein_coding|1/1|c.844G>C|p.Glu282Gln|844/1182|844/1182|282/393||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:548:-49.6551,-4.51545,0
Chromosome	3895727	.	A	C	958.488	.	AB=0;AO=30;DP=30;QA=1095;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|PPE60-Rv3479|Rv3478-Rv3479|intergenic_region|Rv3478-Rv3479|||n.3895727A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1095:-98.8508,-9.0309,0
Chromosome	3898869	.	A	C	1042.71	.	AB=0;AO=34;DP=34;QA=1190;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3479|Rv3479|transcript|Rv3479|protein_coding|1/1|c.3050A>C|p.Asn1017Thr|3050/3066|3050/3066|1017/1021||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1190:-107.396,-10.235,0
Chromosome	3899124	.	G	C	1171.0	.	AB=0;AO=36;DP=36;QA=1334;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3480c|Rv3480c|transcript|Rv3480c|protein_coding|1/1|c.1279C>G|p.Leu427Val|1279/1494|1279/1494|427/497||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1334:-120.355,-10.8371,0
Chromosome	3909235	.	C	G	718.474	.	AB=0;AO=23;DP=24;QA=827;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|otsA|Rv3490|transcript|Rv3490|protein_coding|1/1|c.1000C>G|p.Leu334Val|1000/1503|1000/1503|334/500||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:23:827:-74.5893,-6.92369,0
Chromosome	3922380	.	G	A	864.649	.	AB=0;AO=27;DP=27;QA=989;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|fdxD-fadE26|Rv3503c-Rv3504|intergenic_region|Rv3503c-Rv3504|||n.3922380G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:989:-89.3176,-8.12781,0
Chromosome	3922836	.	C	T	546.804	.	AB=0;AO=18;DP=18;QA=631;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|fadE26|Rv3504|transcript|Rv3504|protein_coding|1/1|c.366C>T|p.Asp122Asp|366/1203|366/1203|122/400||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:631:-57.1053,-5.41854,0
Chromosome	3925733	.	T	G	877.954	.	AB=0;AO=28;DP=28;QA=1007;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|fadD17|Rv3506|transcript|Rv3506|protein_coding|1/1|c.844T>G|p.Phe282Val|844/1509|844/1509|282/502||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1007:-90.9349,-8.42884,0
Chromosome	3969763	.	C	T	634.045	.	AB=0;AO=20;DP=20;QA=744;QR=0;RO=0;TYPE=snp;ANN=T|stop_gained|HIGH|PPE61|Rv3532|transcript|Rv3532|protein_coding|1/1|c.421C>T|p.Gln141*|421/1221|421/1221|141/406||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:744:-67.2862,-6.0206,0
Chromosome	3984321	.	A	G	486.226	.	AB=0;AO=16;DP=16;QA=566;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|cyp125|Rv3545c|transcript|Rv3545c|protein_coding|1/1|c.1125T>C|p.His375His|1125/1302|1125/1302|375/433||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:566:-51.2637,-4.81648,0
Chromosome	3985547	.	G	T	605.285	.	AB=0;AO=20;DP=20;QA=697;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|cyp125-fadA5|Rv3545c-Rv3546|intergenic_region|Rv3545c-Rv3546|||n.3985547G>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:697:-63.0397,-6.0206,0
Chromosome	3989914	.	T	G	525.785	.	AB=0;AO=17;DP=17;QA=605;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3551|Rv3551|transcript|Rv3551|protein_coding|1/1|c.19T>G|p.Ser7Ala|19/879|19/879|7/292||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:605:-54.7737,-5.11751,0
Chromosome	3994898	.	G	A	766.494	.	AB=0;AO=24;DP=24;QA=880;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3555c|Rv3555c|transcript|Rv3555c|protein_coding|1/1|c.802C>T|p.Arg268Trp|802/870|802/870|268/289||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:880:-79.5173,-7.22472,0
Chromosome	4002899	.	C	T	506.428	.	AB=0;AO=17;DP=17;QA=598;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|fadD3|Rv3561|transcript|Rv3561|protein_coding|1/1|c.1263C>T|p.Ala421Ala|1263/1524|1263/1524|421/507||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:598:-54.1404,-5.11751,0
Chromosome	4003130	.	G	A	753.411	.	AB=0;AO=24;DP=24;QA=864;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|fadD3|Rv3561|transcript|Rv3561|protein_coding|1/1|c.1494G>A|p.Val498Val|1494/1524|1494/1524|498/507||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:864:-78.0695,-7.22472,0
Chromosome	4005114	.	C	G	567.647	.	AB=0;AO=18;DP=18;QA=654;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|fadE32|Rv3563|transcript|Rv3563|protein_coding|1/1|c.824C>G|p.Ser275Trp|824/960|824/960|275/319||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:654:-59.1897,-5.41854,0
Chromosome	4008747	.	G	A	643.561	.	AB=0;AO=21;DP=21;QA=752;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|hsaB|Rv3567c|transcript|Rv3567c|protein_coding|1/1|c.536C>T|p.Thr179Ile|536/564|536/564|179/187||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:752:-67.9968,-6.32163,0
Chromosome	4012219	.	C	T	1071.49	.	AB=0;AO=34;DP=34;QA=1221;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|hsaA|Rv3570c|transcript|Rv3570c|protein_coding|1/1|c.52G>A|p.Asp18Asn|52/1185|52/1185|18/394||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1221:-110.173,-10.235,0
Chromosome	4028752	.	G	A	621.175	.	AB=0;AO=20;DP=20;QA=722;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3586|Rv3586|transcript|Rv3586|protein_coding|1/1|c.862G>A|p.Ala288Thr|862/1077|862/1077|288/358||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:722:-65.3002,-6.0206,0
Chromosome	4051716	.	C	T	542.065	.	AB=0;AO=19;DP=19;QA=630;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ftsH|Rv3610c|transcript|Rv3610c|protein_coding|1/1|c.1168G>A|p.Val390Ile|1168/2283|1168/2283|390/760||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:630:-57.0006,-5.71957,0
Chromosome	4054637	.	G	A	697.345	.	AB=0;AO=23;DP=23;QA=801;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|espD|Rv3614c|transcript|Rv3614c|protein_coding|1/1|c.60C>T|p.Gly20Gly|60/555|60/555|20/184||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:801:-72.4038,-6.92369,0
Chromosome	4056124	.	G	A	912.466	.	AB=0;AO=29;DP=29;QA=1051;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|espA|Rv3616c|transcript|Rv3616c|protein_coding|1/1|c.252C>T|p.Leu84Leu|252/1179|252/1179|84/392||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1051:-94.8888,-8.72987,0
Chromosome	4056416	.	A	C	1404.99	.	AB=0;AO=45;DP=45;QA=1590;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|espA-ephA|Rv3616c-Rv3617|intergenic_region|Rv3616c-Rv3617|||n.4056416A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:45:0:0:45:1590:-143.37,-13.5464,0
Chromosome	4060100	.	G	A	333.12	.	AB=0;AO=12;DP=12;QA=427;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|esxV|Rv3619c|transcript|Rv3619c|protein_coding|1/1|c.169C>T|p.Leu57Leu|169/285|169/285|57/94||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:427:-38.7598,-3.61236,0
Chromosome	4061113	.	T	G	628.526	.	AB=0;AO=20;DP=20;QA=736;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|PPE65|Rv3621c|transcript|Rv3621c|protein_coding|1/1|c.777A>C|p.Ala259Ala|777/1242|777/1242|259/413||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:736:-66.5679,-6.0206,0
Chromosome	4063682	.	G	T	923.616	.	AB=0;AO=28;DP=28;QA=1051;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|hpt|Rv3624c|transcript|Rv3624c|protein_coding|1/1|c.223C>A|p.Leu75Met|223/651|223/651|75/216||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1051:-94.8981,-8.42884,0
Chromosome	4067152	.	A	G	685.06	.	AB=0;AO=21;DP=21;QA=786;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3627c|Rv3627c|transcript|Rv3627c|protein_coding|1/1|c.134T>C|p.Val45Ala|134/1386|134/1386|45/461||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:786:-71.0662,-6.32163,0
Chromosome	4078863	.	T	C	769.885	.	AB=0;AO=25;DP=25;QA=879;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3640c|Rv3640c|transcript|Rv3640c|protein_coding|1/1|c.887A>G|p.Glu296Gly|887/1230|887/1230|296/409||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:879:-79.4176,-7.52575,0
Chromosome	4086802	.	G	A	1095.9	.	AB=0;AO=34;DP=34;QA=1248;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|topA|Rv3646c|transcript|Rv3646c|protein_coding|1/1|c.456C>T|p.His152His|456/2805|456/2805|152/934||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1248:-112.617,-10.235,0
Chromosome	4089058	.	C	T	1109.92	.	AB=0;AO=35;DP=35;QA=1262;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3649|Rv3649|transcript|Rv3649|protein_coding|1/1|c.278C>T|p.Pro93Leu|278/2316|278/2316|93/771||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1262:-113.872,-10.5361,0
Chromosome	4091760	.	C	A	1330.61	.	AB=0;AO=43;DP=43;QA=1538;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|PE33-Rv3651|Rv3650-Rv3651|intergenic_region|Rv3650-Rv3651|||n.4091760C>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:43:1538:-138.686,-12.9443,0
Chromosome	4095001	.	CA	C	559.292	.	AB=0;AO=19;DP=19;QA=647;QR=0;RO=0;TYPE=del;ANN=C|frameshift_variant|HIGH|Rv3655c|Rv3655c|transcript|Rv3655c|protein_coding|1/1|c.299delT|p.Leu100fs|299/378|299/378|100/125||;LOF=(Rv3655c|Rv3655c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:647:-58.5416,-5.71957,0
Chromosome	4095295	.	C	T	697.488	.	AB=0;AO=24;DP=24;QA=810;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3655c|Rv3655c|transcript|Rv3655c|protein_coding|1/1|c.6G>A|p.Glu2Glu|6/378|6/378|2/125||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:810:-73.1939,-7.22472,0
Chromosome	4098261	.	G	A	304.229	.	AB=0;AO=10;DP=10;QA=359;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3660c|Rv3660c|transcript|Rv3660c|protein_coding|1/1|c.888C>T|p.Ala296Ala|888/1053|888/1053|296/350||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:359:-32.651,-3.0103,0
Chromosome	4100971	.	C	T	626.892	.	AB=0;AO=20;DP=20;QA=719;QR=0;RO=0;TYPE=snp;ANN=T|intergenic_region|MODIFIER|MTS2823-Rv3662c|RVnc0036a-Rv3662c|intergenic_region|RVnc0036a-Rv3662c|||n.4100971C>T||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:719:-65.034,-6.0206,0
Chromosome	4105757	.	T	C	457.982	.	AB=0;AO=15;DP=15;QA=530;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|dppA|Rv3666c|transcript|Rv3666c|protein_coding|1/1|c.1328A>G|p.Gln443Arg|1328/1626|1328/1626|443/541||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:530:-48.028,-4.51545,0
Chromosome	4107074	.	C	T	1190.22	.	AB=0;AO=37;DP=37;QA=1354;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|dppA|Rv3666c|transcript|Rv3666c|protein_coding|1/1|c.11G>A|p.Arg4Gln|11/1626|11/1626|4/541||	GT:DP:RO:QR:AO:QA:GL	1/1:37:0:0:37:1354:-122.154,-11.1381,0
Chromosome	4112429	.	C	T	681.836	.	AB=0;AO=24;DP=24;QA=791;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3671c|Rv3671c|transcript|Rv3671c|protein_coding|1/1|c.1087G>A|p.Val363Ile|1087/1194|1087/1194|363/397||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:791:-71.4775,-7.22472,0
Chromosome	4115012	.	G	A	824.517	.	AB=0;AO=26;DP=26;QA=956;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3673c|Rv3673c|transcript|Rv3673c|protein_coding|1/1|c.146C>T|p.Thr49Met|146/684|146/684|49/227||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:956:-86.3555,-7.82678,0
Chromosome	4116682	.	C	T	751.718	.	AB=0;AO=23;DP=23;QA=863;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|crp|Rv3676|transcript|Rv3676|protein_coding|1/1|c.205C>T|p.Leu69Leu|205/675|205/675|69/224||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:863:-77.9904,-6.92369,0
Chromosome	4117161	.	A	C	617.108	.	AB=0;AO=19;DP=19;QA=714;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|crp-Rv3677c|Rv3676-Rv3677c|intergenic_region|Rv3676-Rv3677c|||n.4117161A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:714:-64.592,-5.71957,0
Chromosome	4117167	.	GGC	G	560.604	.	AB=0;AO=18;DP=18;QA=659;QR=0;RO=0;TYPE=del;ANN=G|intergenic_region|MODIFIER|crp-Rv3677c|Rv3676-Rv3677c|intergenic_region|Rv3676-Rv3677c|||n.4117168_4117169delGC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:659:-59.6407,-5.41854,0
Chromosome	4119246	.	C	T	813.401	.	AB=0;AO=26;DP=26;QA=935;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3679|Rv3679|transcript|Rv3679|protein_coding|1/1|c.471C>T|p.Asp157Asp|471/1023|471/1023|157/340||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:935:-84.4528,-7.82678,0
Chromosome	4121109	.	A	C	538.404	.	AB=0;AO=17;DP=17;QA=620;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv3680-whiB4|Rv3680-Rv3681c|intergenic_region|Rv3680-Rv3681c|||n.4121109A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:620:-56.1325,-5.11751,0
Chromosome	4121675	.	T	C	449.142	.	AB=0;AO=15;DP=15;QA=533;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|whiB4-ponA2|Rv3681c-Rv3682|intergenic_region|Rv3681c-Rv3682|||n.4121675T>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:533:-48.2946,-4.51545,0
Chromosome	4138377	.	G	A	943.886	.	AB=0;AO=30;DP=30;QA=1087;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|glpK|Rv3696c|transcript|Rv3696c|protein_coding|1/1|c.1379C>T|p.Ala460Val|1379/1554|1379/1554|460/517||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1087:-98.1295,-9.0309,0
Chromosome	4145737	.	G	A	768.456	.	AB=0;AO=25;DP=25;QA=901;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|etgB|Rv3703c|transcript|Rv3703c|protein_coding|1/1|c.1155C>T|p.Tyr385Tyr|1155/1278|1155/1278|385/425||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:901:-81.3967,-7.52575,0
Chromosome	4146314	.	G	T	599.031	.	AB=0;AO=19;DP=19;QA=693;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|etgB|Rv3703c|transcript|Rv3703c|protein_coding|1/1|c.578C>A|p.Pro193Gln|578/1278|578/1278|193/425||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:693:-62.6972,-5.71957,0
Chromosome	4150647	.	C	G	974.76	.	AB=0;AO=31;DP=31;QA=1121;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3707c|Rv3707c|transcript|Rv3707c|protein_coding|1/1|c.394G>C|p.Gly132Arg|394/1011|394/1011|132/336||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1121:-101.196,-9.33193,0
Chromosome	4154051	.	G	A	643.489	.	AB=0;AO=21;DP=21;QA=740;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|leuA|Rv3710|transcript|Rv3710|protein_coding|1/1|c.312G>A|p.Arg104Arg|312/1935|312/1935|104/644||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:740:-66.9104,-6.32163,0
Chromosome	4156239	.	G	A	1006.03	.	AB=0;AO=32;DP=32;QA=1158;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|dnaQ|Rv3711c|transcript|Rv3711c|protein_coding|1/1|c.491C>T|p.Ala164Val|491/990|491/990|164/329||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1158:-104.522,-9.63296,0
Chromosome	4156503	.	T	C	556.487	.	AB=0;AO=18;DP=18;QA=650;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|dnaQ|Rv3711c|transcript|Rv3711c|protein_coding|1/1|c.227A>G|p.Asp76Gly|227/990|227/990|76/329||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:650:-58.8276,-5.41854,0
Chromosome	4158361	.	G	A	836.514	.	AB=0;AO=27;DP=27;QA=955;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|cobQ2|Rv3713|transcript|Rv3713|protein_coding|1/1|c.135G>A|p.Pro45Pro|135/696|135/696|45/231||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:955:-86.2523,-8.12781,0
Chromosome	4179089	.	T	C	521.215	.	AB=0;AO=17;DP=17;QA=601;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3729|Rv3729|transcript|Rv3729|protein_coding|1/1|c.805T>C|p.Ser269Pro|805/2331|805/2331|269/776||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:601:-54.4136,-5.11751,0
Chromosome	4190532	.	C	A	560.954	.	AB=0;AO=20;DP=20;QA=647;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|PPE67-Rv3740c|Rv3739c-Rv3740c|intergenic_region|Rv3739c-Rv3740c|||n.4190532C>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:647:-58.5238,-6.0206,0
Chromosome	4192588	.	G	A	800.091	.	AB=0;AO=26;DP=26;QA=923;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3741c|Rv3741c|transcript|Rv3741c|protein_coding|1/1|c.266C>T|p.Ala89Val|266/675|266/675|89/224||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:923:-83.3815,-7.82678,0
Chromosome	4197137	.	G	GC	667.834	.	AB=0;AO=21;DP=21;QA=766;QR=0;RO=0;TYPE=ins;ANN=GC|intergenic_region|MODIFIER|Rv3747-Rv3748|Rv3747-Rv3748|intergenic_region|Rv3747-Rv3748|||n.4197137_4197138insC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:766:-69.2644,-6.32163,0
Chromosome	4197189	.	G	A	581.961	.	AB=0;AO=18;DP=18;QA=674;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv3747-Rv3748|Rv3747-Rv3748|intergenic_region|Rv3747-Rv3748|||n.4197189G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:674:-60.9934,-5.41854,0
Chromosome	4198611	.	CG	C	520.673	.	AB=0;AO=18;DP=18;QA=610;QR=0;RO=0;TYPE=del;ANN=C|intergenic_region|MODIFIER|Rv3750c-serX|Rv3750c-Rvnt42|intergenic_region|Rv3750c-Rvnt42|||n.4198612delG||||||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:610:-55.0487,-5.41854,0
Chromosome	4200220	.	G	A	828.704	.	AB=0;AO=25;DP=25;QA=945;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3753c|Rv3753c|transcript|Rv3753c|protein_coding|1/1|c.2C>T|p.Thr1Met|2/501|2/501|1/166||WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:945:-85.3665,-7.52575,0
Chromosome	4202383	.	C	A	540.196	.	AB=0;AO=17;DP=17;QA=622;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|proZ|Rv3756c|transcript|Rv3756c|protein_coding|1/1|c.231G>T|p.Val77Val|231/720|231/720|77/239||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:622:-56.3117,-5.11751,0
Chromosome	4205550	.	G	A	782.522	.	AB=0;AO=25;DP=25;QA=896;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3760|Rv3760|transcript|Rv3760|protein_coding|1/1|c.13G>A|p.Val5Met|13/303|13/303|5/100||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:896:-80.9499,-7.52575,0
Chromosome	4207911	.	G	A	978.028	.	AB=0;AO=33;DP=34;QA=1118;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3762c|Rv3762c|transcript|Rv3762c|protein_coding|1/1|c.966C>T|p.Ala322Ala|966/1881|966/1881|322/626||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:33:1118:-100.764,-9.93399,0
Chromosome	4209518	.	T	A	1186.47	.	AB=0;AO=36;DP=36;QA=1355;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|lpqH|Rv3763|transcript|Rv3763|protein_coding|1/1|c.472T>A|p.Cys158Ser|472/480|472/480|158/159||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1355:-122.239,-10.8371,0
Chromosome	4210876	.	C	T	887.734	.	AB=0;AO=29;DP=30;QA=1044;QR=37;RO=1;TYPE=snp;ANN=T|missense_variant|MODERATE|tcrY|Rv3764c|transcript|Rv3764c|protein_coding|1/1|c.134G>A|p.Arg45His|134/1428|134/1428|45/475||	GT:DP:RO:QR:AO:QA:GL	1/1:30:1:37:29:1044:-90.565,-5.33307,0
Chromosome	4212840	.	T	C	872.795	.	AB=0;AO=29;DP=29;QA=1005;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3766|Rv3766|transcript|Rv3766|protein_coding|1/1|c.548T>C|p.Val183Ala|548/690|548/690|183/229||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1005:-90.7472,-8.72987,0
Chromosome	4215484	.	C	G	786.182	.	AB=0;AO=25;DP=25;QA=900;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3770c|Rv3770c|transcript|Rv3770c|protein_coding|1/1|c.292G>C|p.Ala98Pro|292/576|292/576|98/191||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:900:-81.316,-7.52575,0
Chromosome	4216255	.	G	C	1092.74	.	AB=0;AO=34;DP=34;QA=1245;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv3770c-Rv3771c|Rv3770c-Rv3771c|intergenic_region|Rv3770c-Rv3771c|||n.4216255G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1245:-112.349,-10.235,0
Chromosome	4217557	.	G	A	768.507	.	AB=0;AO=25;DP=25;QA=904;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|hisC2|Rv3772|transcript|Rv3772|protein_coding|1/1|c.424G>A|p.Ala142Thr|424/1062|424/1062|142/353||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:904:-81.6764,-7.52575,0
Chromosome	4229087	.	C	T	591.193	.	AB=0;AO=20;DP=20;QA=687;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|glfT1|Rv3782|transcript|Rv3782|protein_coding|1/1|c.741C>T|p.Asn247Asn|741/915|741/915|247/304||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:687:-62.1423,-6.0206,0
Chromosome	4231228	.	G	GT	888.212	.	AB=0;AO=29;DP=30;QA=1017;QR=0;RO=0;TYPE=ins;ANN=GT|frameshift_variant|HIGH|epiB|Rv3784|transcript|Rv3784|protein_coding|1/1|c.975dupT|p.Leu326fs|976/981|976/981|326/326||INFO_REALIGN_3_PRIME	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:29:1017:-91.5165,-8.72987,0
Chromosome	4232327	.	G	A	1036.5	.	AB=0;AO=34;DP=34;QA=1182;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3785|Rv3785|transcript|Rv3785|protein_coding|1/1|c.1008G>A|p.Arg336Arg|1008/1074|1008/1074|336/357||	GT:DP:RO:QR:AO:QA:GL	1/1:34:0:0:34:1182:-106.674,-10.235,0
Chromosome	4232863	.	G	C	508.043	.	AB=0;AO=17;DP=17;QA=593;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3786c|Rv3786c|transcript|Rv3786c|protein_coding|1/1|c.735C>G|p.Asp245Glu|735/1224|735/1224|245/407||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:593:-53.6906,-5.11751,0
Chromosome	4240671	.	T	C	349.47	.	AB=0;AO=12;DP=12;QA=439;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|embC|Rv3793|transcript|Rv3793|protein_coding|1/1|c.809T>C|p.Ile270Thr|809/3285|809/3285|270/1094||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:439:-39.8528,-3.61236,0
Chromosome	4242803	.	G	C	513.363	.	AB=0;AO=16;DP=16;QA=596;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|embC|Rv3793|transcript|Rv3793|protein_coding|1/1|c.2941G>C|p.Val981Leu|2941/3285|2941/3285|981/1094||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:596:-53.9774,-4.81648,0
Chromosome	4243622	.	G	A	290.075	.	AB=0;AO=10;DP=10;QA=347;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|embA|Rv3794|transcript|Rv3794|protein_coding|1/1|c.390G>A|p.Thr130Thr|390/3285|390/3285|130/1094||	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:347:-31.5578,-3.0103,0
Chromosome	4247646	.	C	A	1081.91	.	AB=0;AO=38;DP=38;QA=1296;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|embB|Rv3795|transcript|Rv3795|protein_coding|1/1|c.1133C>A|p.Ala378Glu|1133/3297|1133/3297|378/1098||	GT:DP:RO:QR:AO:QA:GL	1/1:38:0:0:38:1296:-116.916,-11.4391,0
Chromosome	4247729	.	G	A	859.829	.	AB=0;AO=27;DP=27;QA=992;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|embB|Rv3795|transcript|Rv3795|protein_coding|1/1|c.1216G>A|p.Gly406Ser|1216/3297|1216/3297|406/1098||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:992:-89.5879,-8.12781,0
Chromosome	4249408	.	G	A	864.005	.	AB=0;AO=30;DP=30;QA=994;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|embB|Rv3795|transcript|Rv3795|protein_coding|1/1|c.2895G>A|p.Pro965Pro|2895/3297|2895/3297|965/1098||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:994:-89.7464,-9.0309,0
Chromosome	4251297	.	C	G	524.248	.	AB=0;AO=17;DP=17;QA=621;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|fadE35|Rv3797|transcript|Rv3797|protein_coding|1/1|c.213C>G|p.Gly71Gly|213/1782|213/1782|71/593||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:621:-56.2234,-5.11751,0
Chromosome	4261499	.	A	G	531.239	.	AB=0;AO=17;DP=17;QA=611;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|fadD32|Rv3801c|transcript|Rv3801c|protein_coding|1/1|c.1568T>C|p.Val523Ala|1568/1914|1568/1914|523/637||	GT:DP:RO:QR:AO:QA:GL	1/1:17:0:0:17:611:-55.3191,-5.11751,0
Chromosome	4263279	.	G	A	473.416	.	AB=0;AO=15;DP=15;QA=562;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|fadD32-clp6%3B_culp6|Rv3801c-Rv3802c|intergenic_region|Rv3801c-Rv3802c|||n.4263279G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:562:-50.9183,-4.51545,0
Chromosome	4269297	.	G	C	634.165	.	AB=0;AO=19;DP=19;QA=729;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ubiA|Rv3806c|transcript|Rv3806c|protein_coding|1/1|c.537C>G|p.Ile179Met|537/909|537/909|179/302||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:729:-65.9417,-5.71957,0
Chromosome	4269387	.	G	T	573.736	.	AB=0;AO=19;DP=19;QA=666;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ubiA|Rv3806c|transcript|Rv3806c|protein_coding|1/1|c.447C>A|p.Asp149Glu|447/909|447/909|149/302||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:666:-60.2549,-5.71957,0
Chromosome	4269606	.	G	A	977.069	.	AB=0;AO=31;DP=32;QA=1116;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ubiA|Rv3806c|transcript|Rv3806c|protein_coding|1/1|c.228C>T|p.Arg76Arg|228/909|228/909|76/302||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:31:1116:-100.596,-9.33193,0
Chromosome	4270835	.	T	C	509.742	.	AB=0;AO=16;DP=16;QA=592;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|glfT2|Rv3808c|transcript|Rv3808c|protein_coding|1/1|c.1445A>G|p.Gln482Arg|1445/1914|1445/1914|482/637||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:592:-53.6154,-4.81648,0
Chromosome	4275386	.	G	C	882.151	.	AB=0;AO=28;DP=28;QA=1009;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|csp|Rv3811|transcript|Rv3811|protein_coding|1/1|c.589G>C|p.Ala197Pro|589/1620|589/1620|197/539||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1009:-91.1132,-8.42884,0
Chromosome	4287109	.	G	A	980.406	.	AB=0;AO=31;DP=31;QA=1128;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3822|Rv3822|transcript|Rv3822|protein_coding|1/1|c.389G>A|p.Ser130Asn|389/1215|389/1215|130/404||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1128:-101.816,-9.33193,0
Chromosome	4287164	.	G	A	983.999	.	AB=0;AO=31;DP=31;QA=1127;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3822|Rv3822|transcript|Rv3822|protein_coding|1/1|c.444G>A|p.Gly148Gly|444/1215|444/1215|148/404||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1127:-101.73,-9.33193,0
Chromosome	4287361	.	T	C	729.217	.	AB=0;AO=23;DP=23;QA=834;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3822|Rv3822|transcript|Rv3822|protein_coding|1/1|c.641T>C|p.Val214Ala|641/1215|641/1215|214/404||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:834:-75.3724,-6.92369,0
Chromosome	4289953	.	G	A	705.934	.	AB=0;AO=23;DP=23;QA=809;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|mmpL8|Rv3823c|transcript|Rv3823c|protein_coding|1/1|c.1577C>T|p.Ala526Val|1577/3270|1577/3270|526/1089||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:809:-73.1166,-6.92369,0
Chromosome	4290564	.	T	G	423.186	.	AB=0;AO=14;DP=14;QA=495;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|mmpL8|Rv3823c|transcript|Rv3823c|protein_coding|1/1|c.966A>C|p.Ala322Ala|966/3270|966/3270|322/1089||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:495:-44.8813,-4.21442,0
Chromosome	4290827	.	G	C	933.012	.	AB=0;AO=30;DP=30;QA=1075;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|mmpL8|Rv3823c|transcript|Rv3823c|protein_coding|1/1|c.703C>G|p.Arg235Gly|703/3270|703/3270|235/1089||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1075:-97.0422,-9.0309,0
Chromosome	4292305	.	C	T	660.374	.	AB=0;AO=20;DP=20;QA=758;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|papA1|Rv3824c|transcript|Rv3824c|protein_coding|1/1|c.870G>A|p.Met290Ile|870/1536|870/1536|290/511||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:758:-68.5486,-6.0206,0
Chromosome	4302161	.	T	C	1122.69	.	AB=0;AO=35;DP=35;QA=1274;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3827c|Rv3827c|transcript|Rv3827c|protein_coding|1/1|c.629A>G|p.Gln210Arg|629/1227|629/1227|210/408||	GT:DP:RO:QR:AO:QA:GL	1/1:35:0:0:35:1274:-114.955,-10.5361,0
Chromosome	4306472	.	G	T	835.485	.	AB=0;AO=28;DP=28;QA=960;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3832c|Rv3832c|transcript|Rv3832c|protein_coding|1/1|c.340C>A|p.Leu114Met|340/576|340/576|114/191||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:960:-86.688,-8.42884,0
Chromosome	4306767	.	G	A	723.944	.	AB=0;AO=23;DP=23;QA=833;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3832c|Rv3832c|transcript|Rv3832c|protein_coding|1/1|c.45C>T|p.Gly15Gly|45/576|45/576|15/191||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:833:-75.2824,-6.92369,0
Chromosome	4306929	.	G	T	907.447	.	AB=0;AO=29;DP=29;QA=1046;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3833|Rv3833|transcript|Rv3833|protein_coding|1/1|c.63G>T|p.Arg21Arg|63/792|63/792|21/263||	GT:DP:RO:QR:AO:QA:GL	1/1:29:0:0:29:1046:-94.4413,-8.72987,0
Chromosome	4313128	.	T	C	637.11	.	AB=0;AO=21;DP=21;QA=732;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3839|Rv3839|transcript|Rv3839|protein_coding|1/1|c.364T>C|p.Ser122Pro|364/777|364/777|122/258||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:732:-66.192,-6.32163,0
Chromosome	4316566	.	G	C	778.222	.	AB=0;AO=24;DP=24;QA=893;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3843c|Rv3843c|transcript|Rv3843c|protein_coding|1/1|c.31C>G|p.Arg11Gly|31/1029|31/1029|11/342||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:893:-80.6901,-7.22472,0
Chromosome	4318425	.	G	C	495.44	.	AB=0;AO=16;DP=16;QA=594;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|MTS2975-Rv3844|RVnc0040-Rv3844|intergenic_region|RVnc0040-Rv3844|||n.4318425G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:594:-53.7975,-4.81648,0
Chromosome	4323006	.	A	G	433.869	.	AB=0;AO=14;DP=14;QA=515;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3848|Rv3848|transcript|Rv3848|protein_coding|1/1|c.681A>G|p.Ala227Ala|681/909|681/909|227/302||	GT:DP:RO:QR:AO:QA:GL	1/1:14:0:0:14:515:-46.69,-4.21442,0
Chromosome	4323355	.	G	C	671.019	.	AB=0;AO=21;DP=21;QA=774;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv3848-espR|Rv3848-Rv3849|intergenic_region|Rv3848-Rv3849|||n.4323355G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:21:0:0:21:774:-69.9857,-6.32163,0
Chromosome	4329782	.	A	G	620.667	.	AB=0;AO=19;DP=19;QA=717;QR=0;RO=0;TYPE=snp;ANN=G|intergenic_region|MODIFIER|Rv3857c-gltD|Rv3857c-Rv3858c|intergenic_region|Rv3857c-Rv3858c|||n.4329782A>G||||||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:717:-64.8608,-5.71957,0
Chromosome	4334425	.	C	G	902.591	.	AB=0;AO=28;DP=28;QA=1033;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|gltB|Rv3859c|transcript|Rv3859c|protein_coding|1/1|c.1657G>C|p.Glu553Gln|1657/4584|1657/4584|553/1527||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1033:-93.2809,-8.42884,0
Chromosome	4336597	.	A	C	747.545	.	AB=0;AO=25;DP=25;QA=882;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|gltB-Rv3860|Rv3859c-Rv3860|intergenic_region|Rv3859c-Rv3860|||n.4336597A>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:25:0:0:25:882:-79.6856,-7.52575,0
Chromosome	4338595	.	GT	G	454.545	.	AB=0;AO=16;DP=16;QA=545;QR=0;RO=0;TYPE=del;ANN=G|intergenic_region|MODIFIER|whiB6-Rv3863|Rv3862c-Rv3863|intergenic_region|Rv3862c-Rv3863|||n.4338596delT||||||	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:16:545:-49.3633,-4.81648,0
Chromosome	4340006	.	A	C	363.025	.	AB=0;AO=12;DP=12;QA=435;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv3863|Rv3863|transcript|Rv3863|protein_coding|1/1|c.1158A>C|p.Ala386Ala|1158/1179|1158/1179|386/392||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:435:-39.489,-3.61236,0
Chromosome	4357123	.	C	A	601.765	.	AB=0;AO=19;DP=19;QA=697;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|espJ|Rv3878|transcript|Rv3878|protein_coding|1/1|c.431C>A|p.Thr144Lys|431/843|431/843|144/280||	GT:DP:RO:QR:AO:QA:GL	1/1:19:0:0:19:697:-63.0577,-5.71957,0
Chromosome	4359135	.	TGGGGTTCCCGGGGTGATC	T	378.162	.	AB=0;AO=13;DP=13;QA=442;QR=0;RO=0;TYPE=del;ANN=T|disruptive_inframe_deletion|MODERATE|espK|Rv3879c|transcript|Rv3879c|protein_coding|1/1|c.630_647delGATCACCCCGGGAACCCC|p.Ile211_Pro216del|647/2190|630/2190|210/729||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:442:-40.1027,-3.91339,0
Chromosome	4359447	.	A	G	927.718	.	AB=0;AO=30;DP=30;QA=1059;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|espK|Rv3879c|transcript|Rv3879c|protein_coding|1/1|c.336T>C|p.Asn112Asn|336/2190|336/2190|112/729||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1059:-95.6023,-9.0309,0
Chromosome	4367649	.	G	A	969.842	.	AB=0;AO=31;DP=31;QA=1107;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|eccE2|Rv3885c|transcript|Rv3885c|protein_coding|1/1|c.873C>T|p.Tyr291Tyr|873/1614|873/1614|291/537||	GT:DP:RO:QR:AO:QA:GL	1/1:31:0:0:31:1107:-99.9289,-9.33193,0
Chromosome	4372217	.	G	A	821.167	.	AB=0;AO=27;DP=27;QA=938;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3888c|Rv3888c|transcript|Rv3888c|protein_coding|1/1|c.490C>T|p.His164Tyr|490/1026|490/1026|164/341||	GT:DP:RO:QR:AO:QA:GL	1/1:27:0:0:27:938:-84.7175,-8.12781,0
Chromosome	4372353	.	C	G	709.605	.	AB=0;AO=23;DP=23;QA=813;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3888c|Rv3888c|transcript|Rv3888c|protein_coding|1/1|c.354G>C|p.Arg118Arg|354/1026|354/1026|118/341||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:813:-73.4837,-6.92369,0
Chromosome	4374228	.	C	T	1015.6	.	AB=0;AO=32;DP=32;QA=1165;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|esxD|Rv3891c|transcript|Rv3891c|protein_coding|1/1|c.145G>A|p.Ala49Thr|145/324|145/324|49/107||	GT:DP:RO:QR:AO:QA:GL	1/1:32:0:0:32:1165:-105.144,-9.63296,0
Chromosome	4374264	.	G	C	1157.98	.	AB=0;AO=36;DP=36;QA=1318;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|esxD|Rv3891c|transcript|Rv3891c|protein_coding|1/1|c.109C>G|p.Gln37Glu|109/324|109/324|37/107||	GT:DP:RO:QR:AO:QA:GL	1/1:36:0:0:36:1318:-118.908,-10.8371,0
Chromosome	4375480	.	C	T	704.849	.	AB=0;AO=23;DP=23;QA=832;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|PPE69|Rv3892c|transcript|Rv3892c|protein_coding|1/1|c.204G>A|p.Ala68Ala|204/1200|204/1200|68/399||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:832:-75.1919,-6.92369,0
Chromosome	4377033	.	C	G	716.798	.	AB=0;AO=23;DP=23;QA=830;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|eccC2|Rv3894c|transcript|Rv3894c|protein_coding|1/1|c.3420G>C|p.Ser1140Ser|3420/4191|3420/4191|1140/1396||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:830:-75.0115,-6.92369,0
Chromosome	4377909	.	G	A	1369.95	.	AB=0;AO=42;DP=43;QA=1567;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|eccC2|Rv3894c|transcript|Rv3894c|protein_coding|1/1|c.2544C>T|p.Tyr848Tyr|2544/4191|2544/4191|848/1396||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:42:1567:-141.145,-12.6433,0
Chromosome	4383144	.	C	CCGGGG	415.786	.	AB=0;AO=15;DP=16;QA=502;QR=0;RO=0;TYPE=ins;ANN=CCGGGG|frameshift_variant|HIGH|Rv3897c|Rv3897c|transcript|Rv3897c|protein_coding|1/1|c.496_497insCCCCG|p.Gly166fs|496/633|496/633|166/210||;LOF=(Rv3897c|Rv3897c|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:16:0:0:15:502:-45.1553,-4.51545,0
Chromosome	4383655	.	G	A	302.824	.	AB=0;AO=10;DP=10;QA=361;QR=0;RO=0;TYPE=snp;ANN=A|stop_gained&splice_region_variant|HIGH|Rv3898c|Rv3898c|transcript|Rv3898c|protein_coding|1/1|c.331C>T|p.Gln111*|331/333|331/333|111/110||WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:RO:QR:AO:QA:GL	1/1:10:0:0:10:361:-32.8328,-3.0103,0
Chromosome	4384007	.	G	C	767.915	.	AB=0;AO=24;DP=24;QA=888;QR=0;RO=0;TYPE=snp;ANN=C|intergenic_region|MODIFIER|Rv3898c-Rv3899c|Rv3898c-Rv3899c|intergenic_region|Rv3898c-Rv3899c|||n.4384007G>C||||||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:888:-80.2366,-7.22472,0
Chromosome	4384417	.	C	T	303.019	.	AB=0;AO=10;DP=11;QA=364;QR=18;RO=1;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3899c|Rv3899c|transcript|Rv3899c|protein_coding|1/1|c.963G>A|p.Leu321Leu|963/1233|963/1233|321/410||	GT:DP:RO:QR:AO:QA:GL	1/1:11:1:18:10:364:-31.3047,-1.51136,0
Chromosome	4385111	.	G	A	381.066	.	AB=0;AO=13;DP=13;QA=448;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3899c|Rv3899c|transcript|Rv3899c|protein_coding|1/1|c.269C>T|p.Ala90Val|269/1233|269/1233|90/410||	GT:DP:RO:QR:AO:QA:GL	1/1:13:0:0:13:448:-40.6484,-3.91339,0
Chromosome	4385187	.	G	A	343.072	.	AB=0;AO=12;DP=12;QA=416;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3899c|Rv3899c|transcript|Rv3899c|protein_coding|1/1|c.193C>T|p.Pro65Ser|193/1233|193/1233|65/410||	GT:DP:RO:QR:AO:QA:GL	1/1:12:0:0:12:416:-37.7648,-3.61236,0
Chromosome	4386142	.	G	A	610.648	.	AB=0;AO=20;DP=20;QA=702;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3900c|Rv3900c|transcript|Rv3900c|protein_coding|1/1|c.167C>T|p.Ser56Leu|167/936|167/936|56/311||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:702:-63.4932,-6.0206,0
Chromosome	4386709	.	C	T	953.986	.	AB=0;AO=30;DP=30;QA=1085;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3901c|Rv3901c|transcript|Rv3901c|protein_coding|1/1|c.106G>A|p.Ala36Thr|106/450|106/450|36/149||	GT:DP:RO:QR:AO:QA:GL	1/1:30:0:0:30:1085:-97.9473,-9.0309,0
Chromosome	4387074	.	G	A	875.917	.	AB=0;AO=28;DP=28;QA=1002;QR=0;RO=0;TYPE=snp;ANN=A|intergenic_region|MODIFIER|Rv3901c-Rv3902c|Rv3901c-Rv3902c|intergenic_region|Rv3901c-Rv3902c|||n.4387074G>A||||||	GT:DP:RO:QR:AO:QA:GL	1/1:28:0:0:28:1002:-90.4898,-8.42884,0
Chromosome	4394210	.	C	G	580.9	.	AB=0;AO=18;DP=18;QA=675;QR=0;RO=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3909|Rv3909|transcript|Rv3909|protein_coding|1/1|c.19C>G|p.Arg7Gly|19/2409|19/2409|7/802||	GT:DP:RO:QR:AO:QA:GL	1/1:18:0:0:18:675:-61.0848,-5.41854,0
Chromosome	4395387	.	G	A	636.789	.	AB=0;AO=20;DP=20;QA=730;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3909|Rv3909|transcript|Rv3909|protein_coding|1/1|c.1196G>A|p.Ser399Asn|1196/2409|1196/2409|399/802||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:730:-66.0237,-6.0206,0
Chromosome	4400246	.	G	A	787.616	.	AB=0;AO=26;DP=26;QA=902;QR=0;RO=0;TYPE=snp;ANN=A|missense_variant|MODERATE|sigM|Rv3911|transcript|Rv3911|protein_coding|1/1|c.61G>A|p.Asp21Asn|61/669|61/669|21/222||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:902:-81.4812,-7.82678,0
Chromosome	4400660	.	AC	A	422.112	.	AB=0;AO=15;DP=15;QA=494;QR=0;RO=0;TYPE=del;ANN=A|frameshift_variant|HIGH|sigM|Rv3911|transcript|Rv3911|protein_coding|1/1|c.478delC|p.Arg160fs|478/669|478/669|160/222||INFO_REALIGN_3_PRIME;LOF=(sigM|Rv3911|1|1,00)	GT:DP:RO:QR:AO:QA:GL	1/1:15:0:0:15:494:-44.772,-4.51545,0
Chromosome	4407588	.	C	T	733.688	.	AB=0;AO=24;DP=24;QA=846;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|gid|Rv3919c|transcript|Rv3919c|protein_coding|1/1|c.615G>A|p.Ala205Ala|615/675|615/675|205/224||	GT:DP:RO:QR:AO:QA:GL	1/1:24:0:0:24:846:-76.4519,-7.22472,0
Chromosome	4407977	.	C	T	1172.04	.	AB=0;AO=38;DP=38;QA=1331;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|gid|Rv3919c|transcript|Rv3919c|protein_coding|1/1|c.226G>A|p.Gly76Ser|226/675|226/675|76/224||	GT:DP:RO:QR:AO:QA:GL	1/1:38:0:0:38:1331:-120.077,-11.4391,0
Chromosome	4408920	.	GGGT	AGGC	652.755	.	AB=0;AO=22;DP=22;QA=783;QR=0;RO=0;TYPE=complex;ANN=AGGC|intergenic_region|MODIFIER|Rv3920c-Rv3921c|Rv3920c-Rv3921c|intergenic_region|Rv3920c-Rv3921c|||n.4408920_4408923delGGGTinsAGGC||||||	GT:DP:RO:QR:AO:QA:GL	1/1:22:0:0:22:783:-70.4485,-6.62266,0