TB-Profiler result

Run: SRR2101504
Summary

Run ID: SRR2101504

Sample name:

Date: 2025-05-03T08:38:02.200146

Number of reads: 813838

Percentage reads mapped: 99.69

Median coverage: 39.0

Strain: lineage3.1.2;lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.37
lineage4.3 Euro-American (LAM) None 0.58
lineage3.1.2 East-African-Indian RD750 0.35
lineage4.3.4.1 Euro-American (LAM) RD174 0.59
lineage4 Euro-American None 0.63
lineage4.3.4 Euro-American (LAM) RD174 0.64
lineage3.1 East-African-Indian RD750 0.42
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.33 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.5 ethionamide Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.39 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.45 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.61 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 0.46 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.39 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.72 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
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 0.43 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.37 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.28 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 0.41 pyrazinamide Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.45 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
pepQ 2859546 c.873T>G synonymous_variant 0.41 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.63 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.7 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841546 c.-126C>A upstream_gene_variant 0.59 cycloserine Uncertain significance
alr 3841612 c.-193_-192insC upstream_gene_variant 0.6 cycloserine Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.65 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.38 pyrazinamide Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.34 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326181 p.Phe431Leu missense_variant 0.27 ethionamide Uncertain significance
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 0.23 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.71 streptomycin Not assoc w R