TB-Profiler result

Run: SRR29096683
Summary

Run ID: SRR29096683

Sample name:

Date: 2025-02-11T19:25:11.980577

Number of reads: 648123

Percentage reads mapped: 93.05

Median coverage: 18.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.97
lineage1.1 Indo-Oceanic RD239 0.96
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
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 Drugs Confidence
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574712 c.-636A>G upstream_gene_variant 0.35 isoniazid
ethionamide
mshA 574718 c.-630A>G upstream_gene_variant 0.35 isoniazid
ethionamide
mshA 574724 c.-624T>C upstream_gene_variant 0.35 isoniazid
ethionamide
mshA 574731 c.-617A>G upstream_gene_variant 0.32 isoniazid
ethionamide
mshA 574739 c.-609T>C upstream_gene_variant 0.3 isoniazid
ethionamide
mshA 574743 c.-605_-603delCGGinsGGC upstream_gene_variant 0.3 isoniazid
ethionamide
ccsA 620319 c.429C>G synonymous_variant 0.29 kanamycin
capreomycin
amikacin
ccsA 620340 c.450C>G synonymous_variant 0.3 kanamycin
capreomycin
amikacin
ccsA 620349 c.459A>G synonymous_variant 0.32 kanamycin
capreomycin
amikacin
ccsA 620362 p.Ala158Thr missense_variant 0.3 kanamycin
capreomycin
amikacin
ccsA 620367 c.477T>C synonymous_variant 0.29 kanamycin
capreomycin
amikacin
ccsA 620373 c.483C>G synonymous_variant 0.27 kanamycin
capreomycin
amikacin
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.91 rifampicin Not assoc w R
rpoB 760196 c.390C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 760490 c.684C>T synonymous_variant 0.94 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.89 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.89 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.95 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.9 bedaquiline Uncertain significance
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781808 c.249C>T synonymous_variant 0.29 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.29 streptomycin
rpsL 781820 c.261G>C synonymous_variant 0.3 streptomycin
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
fbiC 1304826 c.1896G>C synonymous_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1304829 c.1899T>C synonymous_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>G synonymous_variant 0.25 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304916 c.1986T>C synonymous_variant 0.44 pretomanid
delamanid
clofazimine
fbiC 1304940 c.2010A>G synonymous_variant 0.35 pretomanid
delamanid
clofazimine
fbiC 1304955 c.2025G>A synonymous_variant 0.39 pretomanid
delamanid
clofazimine
fbiC 1304958 c.2028T>G synonymous_variant 0.37 pretomanid
delamanid
clofazimine
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674663 c.462G>C synonymous_variant 0.3 isoniazid
ethionamide
inhA 1674669 c.468G>C synonymous_variant 0.29 isoniazid
ethionamide
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918053 c.114G>A synonymous_variant 1.0 capreomycin
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.7 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518570 c.456G>C synonymous_variant 0.44 isoniazid
kasA 2518574 p.Ile154Val missense_variant 0.44 isoniazid
kasA 2518579 c.465T>C synonymous_variant 0.41 isoniazid
kasA 2518588 c.474T>C synonymous_variant 0.44 isoniazid
kasA 2518594 c.480C>G synonymous_variant 0.38 isoniazid
kasA 2518597 c.483C>G synonymous_variant 0.41 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.39 isoniazid
kasA 2518639 c.525G>C synonymous_variant 0.37 isoniazid
kasA 2518657 c.543G>C synonymous_variant 0.44 isoniazid
kasA 2518663 c.549T>C synonymous_variant 0.4 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.4 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
Rv2477c 2783013 c.1030T>C synonymous_variant 0.44 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783015 p.Ser343Thr missense_variant 0.44 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783020 c.1023G>C synonymous_variant 0.44 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783040 p.Ala335Thr missense_variant 0.54 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2783044 c.999G>A synonymous_variant 0.54 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783059 c.984T>C synonymous_variant 0.46 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783062 c.981C>G synonymous_variant 0.46 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783077 c.966T>C synonymous_variant 0.43 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783080 c.963G>C synonymous_variant 0.43 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783092 c.951A>G synonymous_variant 0.4 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin
pepQ 2860179 c.240G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv2681 2996912 c.174C>T synonymous_variant 0.85 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3066118 p.Asn25Ser missense_variant 0.32 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066150 c.42C>T synonymous_variant 0.29 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625621 c.-711G>C upstream_gene_variant 0.32 rifampicin
bedaquiline
mtrB 3625633 c.981C>T synonymous_variant 0.67 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625648 c.-738T>C upstream_gene_variant 0.3 rifampicin
bedaquiline
lpqB 3625654 c.-746_-744delTTGinsCTC upstream_gene_variant 0.27 rifampicin
bedaquiline
lpqB 3625663 c.-753G>C upstream_gene_variant 0.29 rifampicin
bedaquiline
lpqB 3625675 c.-765G>C upstream_gene_variant 0.29 rifampicin
bedaquiline
mtrB 3626467 c.147G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626840 c.-227C>G upstream_gene_variant 0.37 rifampicin
bedaquiline
mtrA 3626846 c.504G>A synonymous_variant 0.37 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626858 c.-245A>G upstream_gene_variant 0.41 rifampicin
bedaquiline
mtrB 3626866 c.-253T>C upstream_gene_variant 0.41 rifampicin
bedaquiline
mtrB 3626890 c.-277T>C upstream_gene_variant 0.37 rifampicin
bedaquiline
mtrB 3626891 c.-278G>C upstream_gene_variant 0.35 rifampicin
bedaquiline
mtrB 3626903 c.-290T>C upstream_gene_variant 0.43 rifampicin
bedaquiline
mtrA 3626912 c.438T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626924 c.-311G>C upstream_gene_variant 0.5 rifampicin
bedaquiline
mtrB 3626930 c.-317A>G upstream_gene_variant 0.48 rifampicin
bedaquiline
mtrA 3626939 c.411A>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877613 p.Ile299Val missense_variant 0.25 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.21 rifampicin
clpC1 4038812 c.1893T>C synonymous_variant 0.48 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.29 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.29 pyrazinamide
clpC1 4039338 p.Thr456Gln missense_variant 0.26 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
panD 4044725 c.-444C>T upstream_gene_variant 0.39 pyrazinamide
panD 4044737 c.-456T>G upstream_gene_variant 0.39 pyrazinamide
panD 4044740 c.-459C>T upstream_gene_variant 0.56 pyrazinamide
panD 4044755 c.-474G>C upstream_gene_variant 0.42 pyrazinamide
panD 4044779 c.-500_-498delCTAinsTGC upstream_gene_variant 0.4 pyrazinamide
panD 4044785 c.-504C>G upstream_gene_variant 0.39 pyrazinamide
panD 4044788 c.-507G>C upstream_gene_variant 0.39 pyrazinamide
panD 4044791 c.-510G>C upstream_gene_variant 0.38 pyrazinamide
panD 4044806 c.-525T>C upstream_gene_variant 0.38 pyrazinamide
panD 4044812 c.-531A>G upstream_gene_variant 0.38 pyrazinamide
panD 4044815 c.-534G>A upstream_gene_variant 0.38 pyrazinamide
panD 4044821 c.-540C>T upstream_gene_variant 0.38 pyrazinamide
panD 4044833 c.-552A>C upstream_gene_variant 0.38 pyrazinamide
panD 4044839 c.-558C>G upstream_gene_variant 0.38 pyrazinamide
panD 4044844 c.-563T>C upstream_gene_variant 0.37 pyrazinamide
panD 4044854 c.-573A>G upstream_gene_variant 0.34 pyrazinamide
panD 4044965 c.-684T>C upstream_gene_variant 0.23 pyrazinamide
panD 4044972 c.-691A>G upstream_gene_variant 0.24 pyrazinamide
panD 4044977 c.-696T>C upstream_gene_variant 0.28 pyrazinamide
panD 4044983 c.-702G>C upstream_gene_variant 0.3 pyrazinamide
panD 4044989 c.-708T>C upstream_gene_variant 0.29 pyrazinamide
panD 4044995 c.-714A>G upstream_gene_variant 0.3 pyrazinamide
panD 4045000 c.-719A>C upstream_gene_variant 0.3 pyrazinamide
panD 4045022 c.-742_-741delTCinsCG upstream_gene_variant 0.3 pyrazinamide
panD 4045025 c.-744C>G upstream_gene_variant 0.32 pyrazinamide
panD 4045028 c.-747C>G upstream_gene_variant 0.32 pyrazinamide
panD 4045052 c.-771G>C upstream_gene_variant 0.32 pyrazinamide
panD 4045055 c.-774T>C upstream_gene_variant 0.32 pyrazinamide
panD 4045063 c.-782T>C upstream_gene_variant 0.33 pyrazinamide
panD 4045064 c.-785_-783delGCGinsACC upstream_gene_variant 0.33 pyrazinamide
panD 4045076 c.-795A>C upstream_gene_variant 0.36 pyrazinamide
panD 4045088 c.-807T>C upstream_gene_variant 0.32 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240771 c.909G>C synonymous_variant 0.38 ethambutol
embC 4240780 c.918T>C synonymous_variant 0.33 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.33 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.33 ethambutol
embC 4240819 c.957A>G synonymous_variant 0.32 ethambutol
embC 4240822 c.960C>G synonymous_variant 0.32 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.33 ethambutol
embC 4241042 p.Asn394Asp missense_variant 0.92 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.95 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.97 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R