TB-Profiler result

Run: SRR6045448
Summary

Run ID: SRR6045448

Sample name:

Date: 2025-09-15T19:07:46.511806

Number of reads: 1857971

Percentage reads mapped: 75.93

Median coverage: 61.0

Strain: lineage2.2;lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2.2 East-Asian (Beijing) RD105;RD207 41.51
lineage3 East-African-Indian RD750 60.27
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
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 8405 p.His368Gln missense_variant 0.67 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.97 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.51 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.51 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.23 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.68 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.58 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.46 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 775675 p.Trp936Arg missense_variant 0.46 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.23 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 778588 p.Gln106His missense_variant 0.12 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
fbiC 1305215 p.Ser762Asn missense_variant 0.66 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
sigE 1364706 c.294G>A synonymous_variant 0.35 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.5 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1416934 c.414G>A synonymous_variant 0.73 ethambutol Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.34 pyrazinamide Not assoc w R - Interim
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
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.66 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.59 pyrazinamide Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 0.61 isoniazid Not assoc w R
folC 2746268 p.Thr444Ile missense_variant 0.48 para-aminosalicylic_acid Uncertain significance
Rv2477c 2782498 c.1545C>T synonymous_variant 0.69 amikacin Not assoc w R
ethambutol Not assoc w R
kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
Rv2477c 2783834 p.Val70Ala missense_variant 0.93 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
pepQ 2859624 c.795G>A synonymous_variant 0.64 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv2681 2996975 c.237G>A synonymous_variant 0.66 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.39 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.49 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640671 c.129T>C synonymous_variant 0.55 clofazimine Not assoc w R - Interim
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.55 pyrazinamide Uncertain significance
glpK 4138622 c.1134C>T synonymous_variant 0.49 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
glpK 4139067 p.Glu230Ala missense_variant 0.58 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.56 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.39 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.35 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.4 streptomycin Not assoc w R