TB-Profiler result

Run: SRR6650106
Summary

Run ID: SRR6650106

Sample name:

Date: 15-08-2023 08:19:47

Number of reads: 961235

Percentage reads mapped: 99.4

Strain: lineage3

Drug-resistance: Other

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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 R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
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
lineage3 East-African-Indian CAS RD750 1.0
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 6654 p.Asp472Gly missense_variant 0.17
gyrA 6898 c.-404G>C upstream_gene_variant 0.2
gyrA 6910 c.-392G>A upstream_gene_variant 0.18
gyrA 6922 c.-380G>T upstream_gene_variant 0.18
gyrB 6927 p.Leu563Trp missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8044 p.Arg248Pro missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490975 p.Thr65Pro missense_variant 0.25
fgd1 491008 p.Thr76Pro missense_variant 0.33
fgd1 491014 p.Thr78Pro missense_variant 0.44
fgd1 491027 p.Asn82Thr missense_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576705 p.Gln453Pro missense_variant 0.18
mshA 576723 p.Val459Gly missense_variant 0.3
ccsA 619707 c.-184T>G upstream_gene_variant 0.23
ccsA 620532 c.642T>G synonymous_variant 0.23
ccsA 620537 p.Val216Gly missense_variant 0.18
ccsA 620748 c.858T>G synonymous_variant 0.19
ccsA 620752 p.Arg288Gly missense_variant 0.17
ccsA 620756 p.Asp289Gly missense_variant 0.24
rpoB 759611 c.-196G>C upstream_gene_variant 0.17
rpoB 759615 c.-192A>C upstream_gene_variant 0.2
rpoB 759620 c.-187A>C upstream_gene_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763849 c.480G>A synonymous_variant 0.17
rpoC 766900 c.3531T>G synonymous_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781531 c.-29T>G upstream_gene_variant 0.15
rplC 801274 p.Thr156Pro missense_variant 0.21
rplC 801279 c.471G>C synonymous_variant 0.19
rplC 801287 p.Val160Gly missense_variant 0.29
rplC 801316 p.Met170Val missense_variant 0.19
fbiC 1302903 c.-28T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.25
atpE 1461087 p.Leu15Val missense_variant 0.2
atpE 1461108 p.Ile22Leu missense_variant 0.2
atpE 1461131 c.87T>G synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673679 c.-523T>G upstream_gene_variant 0.18
fabG1 1674076 p.Thr213Pro missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.27
ndh 2103235 c.-193C>G upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169317 c.1296C>T synonymous_variant 0.16
PPE35 2170066 p.Ala183Pro missense_variant 0.27
PPE35 2170072 p.Gly181Arg missense_variant 0.15
PPE35 2170383 p.Ala77Gly missense_variant 0.17
PPE35 2170390 p.Trp75Gly missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2715032 p.Cys101Gly missense_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.15
ahpC 2726277 p.Lys29Gln missense_variant 0.21
ahpC 2726286 p.Gly32Arg missense_variant 0.21
ahpC 2726338 p.Val49Gly missense_variant 0.15
pepQ 2859358 p.Thr354Asn missense_variant 0.15
pepQ 2859377 p.Thr348Ala missense_variant 0.18
pepQ 2859414 c.1005T>G synonymous_variant 0.22
pepQ 2859421 p.Arg333Pro missense_variant 0.2
pepQ 2859454 p.Val322Gly missense_variant 0.25
ribD 2987323 p.Val162Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.18
fbiD 3339626 p.His170Pro missense_variant 0.33
fbiD 3339688 p.Thr191Pro missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.25
fbiB 3641633 c.99C>G synonymous_variant 0.14
alr 3841349 c.72C>T synonymous_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243264 p.Arg11Gln missense_variant 0.94
embA 4243372 p.Gln47Arg missense_variant 0.15
embA 4243398 p.Thr56Pro missense_variant 0.18
embA 4246365 p.Tyr1045Asp missense_variant 0.12
embB 4247616 p.Glu368Gly missense_variant 0.24
embB 4249403 p.Thr964Pro missense_variant 0.15
ubiA 4269455 p.Val127Leu missense_variant 0.12
ubiA 4269848 c.-15A>G upstream_gene_variant 0.19
ethA 4326905 p.Leu190Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0