TB-Profiler result

Run: SRR6650401
Summary

Run ID: SRR6650401

Sample name:

Date: 15-08-2023 08:23:53

Number of reads: 652993

Percentage reads mapped: 99.28

Strain: lineage1.2.2.2

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA RD239 0.99
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6645 p.Ser469Asn missense_variant 0.18
gyrA 7268 c.-34C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9289 p.Val663Gly missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491008 p.Thr76Pro missense_variant 0.36
fgd1 491014 p.Thr78Pro missense_variant 0.5
fgd1 491018 p.Phe79Ser missense_variant 0.2
fgd1 491027 p.Asn82Thr missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576321 p.Val325Gly missense_variant 0.22
mshA 576723 p.Val459Gly missense_variant 0.3
ccsA 619835 c.-56G>T upstream_gene_variant 0.25
ccsA 619839 c.-52C>G upstream_gene_variant 0.18
ccsA 620752 p.Arg288Gly missense_variant 0.22
ccsA 620756 p.Asp289Gly missense_variant 0.22
rpoB 759795 c.-12G>A upstream_gene_variant 0.18
rpoB 759811 p.Ala2Glu missense_variant 0.2
rpoB 759816 p.Ser4Pro missense_variant 0.2
rpoB 762824 p.Asp1006Glu missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.86
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775603 p.Thr960Pro missense_variant 0.33
mmpL5 775625 p.Trp952Cys missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775643 c.2838A>C synonymous_variant 0.21
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.25
mmpR5 779336 p.Asp116Ala missense_variant 0.23
mmpR5 779346 p.Asp119Glu missense_variant 0.38
mmpR5 779348 p.Val120Gly missense_variant 0.46
mmpR5 779354 p.Leu122Arg missense_variant 0.19
mmpR5 779356 p.Arg123Gly missense_variant 0.38
mmpR5 779363 p.Leu125Arg missense_variant 0.38
mmpR5 779371 p.Ala128Pro missense_variant 0.33
rpsL 781363 c.-197T>G upstream_gene_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801274 p.Thr156Pro missense_variant 0.29
rplC 801287 p.Val160Gly missense_variant 0.67
rplC 801316 p.Met170Val missense_variant 0.33
fbiC 1303199 p.Val90Gly missense_variant 0.19
fbiC 1304435 p.Ala502Gly missense_variant 0.25
fbiC 1304438 p.Glu503Gly missense_variant 0.33
Rv1258c 1406452 p.Thr297Pro missense_variant 0.29
Rv1258c 1407075 p.Val89Gly missense_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473921 n.264A>G non_coding_transcript_exon_variant 0.29
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.27
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.67
fabG1 1673690 p.Val84Gly missense_variant 0.2
fabG1 1674076 p.Thr213Pro missense_variant 0.55
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918029 c.90C>A synonymous_variant 0.2
tlyA 1918065 c.126G>C synonymous_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169293 c.1320T>G synonymous_variant 0.33
PPE35 2169299 p.Asn438Lys missense_variant 0.22
PPE35 2169317 c.1296C>T synonymous_variant 0.67
PPE35 2169320 p.Leu431Phe missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289386 c.-145A>C upstream_gene_variant 0.27
pncA 2289500 c.-259A>G upstream_gene_variant 0.2
pncA 2289509 c.-268A>G upstream_gene_variant 0.21
pncA 2289511 c.-270T>G upstream_gene_variant 0.42
pncA 2290198 c.-957C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.18
kasA 2518151 p.Ser13Arg missense_variant 0.2
kasA 2518155 p.Val14Gly missense_variant 0.18
kasA 2518605 p.Val164Gly missense_variant 0.29
eis 2715396 c.-64G>T upstream_gene_variant 0.2
eis 2715413 c.-81G>C upstream_gene_variant 0.3
eis 2715560 c.-228T>G upstream_gene_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.22
ahpC 2726269 p.Val26Gly missense_variant 0.22
ahpC 2726277 p.Lys29Gln missense_variant 0.44
ahpC 2726286 p.Gly32Arg missense_variant 0.36
folC 2746745 p.Val285Gly missense_variant 0.18
pepQ 2859340 p.Glu360Gly missense_variant 0.23
pepQ 2859367 p.Met351Lys missense_variant 0.25
pepQ 2859377 p.Thr348Ala missense_variant 0.56
pepQ 2859414 c.1005T>G synonymous_variant 0.18
pepQ 2859438 c.981T>G synonymous_variant 0.17
pepQ 2859454 p.Val322Gly missense_variant 0.18
Rv2752c 3066181 p.Asp4Ala missense_variant 0.18
thyX 3067995 c.-50A>C upstream_gene_variant 0.31
thyX 3068024 c.-79A>C upstream_gene_variant 0.2
thyX 3068031 c.-86A>C upstream_gene_variant 0.2
thyX 3068042 c.-97T>C upstream_gene_variant 0.25
thyX 3068051 c.-106A>C upstream_gene_variant 0.18
thyA 3073811 p.Ser221Gly missense_variant 0.15
thyA 3073842 p.Asp210Glu missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087670 p.Asp284Ala missense_variant 0.18
fbiD 3339153 p.Leu12Phe missense_variant 0.22
fbiD 3339160 p.Ala15Pro missense_variant 0.22
fbiD 3339273 c.156T>G synonymous_variant 0.46
fbiD 3339279 c.162T>G synonymous_variant 0.46
fbiD 3339292 p.Ile59Val missense_variant 0.2
fbiD 3339310 p.Asp65His missense_variant 0.33
fbiD 3339688 p.Thr191Pro missense_variant 0.31
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.14
Rv3236c 3612356 p.Glu254Gly missense_variant 0.23
Rv3236c 3612381 c.736C>T synonymous_variant 0.29
Rv3236c 3612388 c.729T>G synonymous_variant 0.47
Rv3236c 3612813 p.Thr102Pro missense_variant 0.18
Rv3236c 3613168 c.-52A>G upstream_gene_variant 1.0
fbiA 3640738 p.Met66Leu missense_variant 1.0
alr 3840402 p.Arg340Leu missense_variant 1.0
rpoA 3878248 p.Ser87Trp missense_variant 0.2
rpoA 3878301 c.207C>A synonymous_variant 0.24
ddn 3987090 p.Glu83Gln missense_variant 1.0
clpC1 4039448 c.1257A>C synonymous_variant 0.18
clpC1 4039451 c.1254G>C synonymous_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.25
clpC1 4039890 p.Val272Gly missense_variant 0.27
clpC1 4039916 c.789T>G synonymous_variant 0.28
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.4
embC 4239998 p.Ala46Pro missense_variant 0.25
embC 4240001 p.Thr47Pro missense_variant 0.25
embC 4240006 c.144A>C synonymous_variant 0.42
embC 4240008 p.Leu49Pro missense_variant 0.18
embC 4240017 p.Val52Gly missense_variant 0.18
embC 4240520 p.Thr220Pro missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.25
embA 4243888 p.Val219Gly missense_variant 0.15
embA 4244638 p.Val469Gly missense_variant 0.2
embA 4244641 p.Val470Gly missense_variant 0.3
embA 4244650 p.Asp473Gly missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247629 c.1116C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248689 p.Ile726Val missense_variant 0.21
embB 4248799 c.2286T>G synonymous_variant 0.2
embB 4249403 p.Thr964Pro missense_variant 0.33
aftB 4268776 p.Ser21Gly missense_variant 0.29
aftB 4268907 c.-71T>C upstream_gene_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269490 p.Ala115Gly missense_variant 0.25
ubiA 4269502 p.Val111Gly missense_variant 0.22
aftB 4269504 c.-668A>G upstream_gene_variant 0.22
ubiA 4269511 p.Val108Gly missense_variant 0.25
ubiA 4269514 p.Val107Gly missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269848 c.-15A>G upstream_gene_variant 0.22
ubiA 4269864 c.-31C>G upstream_gene_variant 0.43
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4326887 p.Asp196Gly missense_variant 0.31
ethR 4326907 c.-642C>G upstream_gene_variant 0.21
ethR 4327597 p.Thr17Pro missense_variant 0.18
ethR 4327624 p.Glu26Lys missense_variant 0.17
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0