##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20240531
##source=freeBayes v1.3.2-dirty
##reference=reference/ref.fa
##contig=<ID=Chromosome,length=4411532>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region Chromosome:0-1495040"
##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=1.13+htslib-1.13
##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Fri May 31 19:43:23 2024
##bcftools_annotateVersion=1.13+htslib-1.13
##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=Fri May 31 19:43:24 2024
##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -noStats -no-downstream -no-upstream -no-utr ref snps.filt.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	rif_resistant_fastq_gz
Chromosome	15890	.	G	A	1500.92	.	AB=0;AO=48;DP=48;QA=1704;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0014c|GENE_Rv0014c|transcript|TRANSCRIPT_Rv0014c|protein_coding|1/1|c.1581C>T|p.Ser527Ser|1581/1881|1581/1881|527/626||	GT:DP:RO:QR:AO:QA:GL	1/1:48:0:0:48:1704:-153.63,-14.4494,0
Chromosome	154990	.	G	T	1358.62	.	AB=0;AO=45;DP=45;QA=1558;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0127|GENE_Rv0127|transcript|TRANSCRIPT_Rv0127|protein_coding|1/1|c.759G>T|p.Arg253Arg|759/1368|759/1368|253/455||	GT:DP:RO:QR:AO:QA:GL	1/1:45:0:0:45:1558:-140.494,-13.5464,0
Chromosome	346693	.	G	T	635.034	.	AB=0;AO=20;DP=20;QA=729;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0284|GENE_Rv0284|transcript|TRANSCRIPT_Rv0284|protein_coding|1/1|c.1059G>T|p.Ser353Ser|1059/3993|1059/3993|353/1330||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:729:-65.9317,-6.0206,0
Chromosome	449194	.	G	A	651.409	.	AB=0;AO=23;DP=23;QA=782;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0372c|GENE_Rv0372c|transcript|TRANSCRIPT_Rv0372c|protein_coding|1/1|c.192C>T|p.Gly64Gly|192/756|192/756|64/251||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:782:-70.6929,-6.92369,0
Chromosome	497491	.	G	A	1816.74	.	AB=0;AO=56;DP=56;QA=2057;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0411c|GENE_Rv0411c|transcript|TRANSCRIPT_Rv0411c|protein_coding|1/1|c.810C>T|p.Asp270Asp|810/987|810/987|270/328||	GT:DP:RO:QR:AO:QA:GL	1/1:56:0:0:56:2057:-185.366,-16.8577,0
Chromosome	761110	.	A	T	1500.1	.	AB=0;AO=47;DP=48;QA=1701;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0667|GENE_Rv0667|transcript|TRANSCRIPT_Rv0667|protein_coding|1/1|c.1304A>T|p.Asp435Val|1304/3519|1304/3519|435/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:48:0:0:47:1701:-153.05,-14.1484,0
Chromosome	811753	.	C	T	1585.34	.	AB=0;AO=48;DP=48;QA=1796;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0715|GENE_Rv0715|transcript|TRANSCRIPT_Rv0715|protein_coding|1/1|c.12C>T|p.His4His|12/318|12/318|4/105||	GT:DP:RO:QR:AO:QA:GL	1/1:48:0:0:48:1796:-161.892,-14.4494,0
Chromosome	1565566	.	C	T	1332.75	.	AB=0;AO=43;DP=43;QA=1534;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1391|GENE_Rv1391|transcript|TRANSCRIPT_Rv1391|protein_coding|1/1|c.126C>T|p.Pro42Pro|126/1257|126/1257|42/418||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:43:1534:-138.344,-12.9443,0
Chromosome	1834177	.	A	C	1769.09	.	AB=0;AO=54;DP=54;QA=2006;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1630|GENE_Rv1630|transcript|TRANSCRIPT_Rv1630|protein_coding|1/1|c.636A>C|p.Arg212Arg|636/1446|636/1446|212/481||	GT:DP:RO:QR:AO:QA:GL	1/1:54:0:0:54:2006:-180.776,-16.2556,0
Chromosome	1849051	.	C	T	2143.76	.	AB=0;AO=65;DP=65;QA=2415;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1640c|GENE_Rv1640c|transcript|TRANSCRIPT_Rv1640c|protein_coding|1/1|c.2985G>A|p.Pro995Pro|2985/3519|2985/3519|995/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:65:0:0:65:2415:-217.563,-19.567,0
Chromosome	2505085	.	G	A	1199.98	.	AB=0;AO=39;DP=39;QA=1425;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2231c|GENE_Rv2231c|transcript|TRANSCRIPT_Rv2231c|protein_coding|1/1|c.615C>T|p.Ala205Ala|615/1095|615/1095|205/364||	GT:DP:RO:QR:AO:QA:GL	1/1:39:0:0:39:1425:-128.53,-11.7402,0
Chromosome	2543395	.	T	C	1871.23	.	AB=0;AO=58;DP=58;QA=2110;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2268c|GENE_Rv2268c|transcript|TRANSCRIPT_Rv2268c|protein_coding|1/1|c.882A>G|p.Glu294Glu|882/1470|882/1470|294/489||	GT:DP:RO:QR:AO:QA:GL	1/1:58:0:0:58:2110:-190.142,-17.4597,0
Chromosome	2640807	.	G	A	1341.77	.	AB=0;AO=43;DP=43;QA=1519;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2357c|GENE_Rv2357c|transcript|TRANSCRIPT_Rv2357c|protein_coding|1/1|c.258C>T|p.Val86Val|258/1392|258/1392|86/463||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:43:1519:-136.983,-12.9443,0
Chromosome	2775361	.	C	T	2221.3	.	AB=0;AO=69;DP=69;QA=2506;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2472|GENE_Rv2472|transcript|TRANSCRIPT_Rv2472|protein_coding|1/1|c.90C>T|p.Arg30Arg|90/294|90/294|30/97||	GT:DP:RO:QR:AO:QA:GL	1/1:69:0:0:69:2506:-225.745,-20.7711,0
Chromosome	2789798	.	G	T	2050.68	.	AB=0;AO=62;DP=62;QA=2312;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2483c|GENE_Rv2483c|transcript|TRANSCRIPT_Rv2483c|protein_coding|1/1|c.1225C>A|p.Arg409Arg|1225/1743|1225/1743|409/580||	GT:DP:RO:QR:AO:QA:GL	1/1:62:0:0:62:2312:-208.29,-18.6639,0
Chromosome	3477942	.	A	G	2414.91	.	AB=0;AO=75;DP=75;QA=2721;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3109|GENE_Rv3109|transcript|TRANSCRIPT_Rv3109|protein_coding|1/1|c.294A>G|p.Thr98Thr|294/1080|294/1080|98/359||	GT:DP:RO:QR:AO:QA:GL	1/1:75:0:0:75:2721:-245.092,-22.5773,0
Chromosome	3587446	.	G	A	1562.41	.	AB=0;AO=49;DP=49;QA=1766;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3210c|GENE_Rv3210c|transcript|TRANSCRIPT_Rv3210c|protein_coding|1/1|c.94C>T|p.Leu32Leu|94/696|94/696|32/231||	GT:DP:RO:QR:AO:QA:GL	1/1:49:0:0:49:1766:-159.195,-14.7505,0
Chromosome	4254431	.	G	A	1391.26	.	AB=0;AO=46;DP=46;QA=1617;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1518C>T|p.Asp506Asp|1518/1569|1518/1569|506/522||	GT:DP:RO:QR:AO:QA:GL	1/1:46:0:0:46:1617:-145.801,-13.8474,0
Chromosome	4254477	.	T	C	760.909	.	AB=0;AO=26;DP=26;QA=933;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1472A>G|p.His491Arg|1472/1569|1472/1569|491/522||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:933:-84.2834,-7.82678,0