TB-Profiler result

Run: SRR13861485
Summary

Run ID: SRR13861485

Sample name:

Date: 2025-09-15T16:24:19.940455

Number of reads: 1411192

Percentage reads mapped: 28.25

Median coverage: 48.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.9 Euro-American (H37Rv-like) None 100.0
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
dnaA 715 p.Thr239Pro missense_variant 1.0 isoniazid Uncertain significance
fgd1 490955 p.Met58Arg missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 574818 c.-530G>C upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
hadA 731861 c.-69G>C upstream_gene_variant 1.0 isoniazid Uncertain significance
rpsL 781155 c.-405G>A upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1304529 c.1599T>C synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406845 p.Ala166Pro missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
inhA 1674607 p.Pro136Ser missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674778 p.Pro193Ala missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833269 c.-273G>T upstream_gene_variant 1.0 pyrazinamide Uncertain significance
bacA 2064115 p.Ala205Asp missense_variant 0.98 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2169081 p.Leu511Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169202 p.Ser471Pro missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222091 c.1074G>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223306 c.-142T>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pncA 2289228 p.Ile5Asn missense_variant 1.0 pyrazinamide Uncertain significance
kasA 2518176 p.Ala21Gly missense_variant 1.0 isoniazid Uncertain significance
eis 2714755 p.Pro193Gln missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726324 c.132A>G synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ahpC 2726362 p.Phe57Ser missense_variant 1.0 isoniazid Uncertain significance
pepQ 2859580 p.Leu280Arg missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pepQ 2859999 c.420G>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2681 2997338 c.600G>C synonymous_variant 1.0 capreomycin Uncertain significance
thyX 3067940 c.6C>G synonymous_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyA 3074620 c.-149C>A upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
mtrB 3626051 p.Ser188Trp missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
ddn 3986889 p.Phe16Val missense_variant 1.0 delamanid Uncertain significance
pretomanid Uncertain significance
embC 4242041 p.Met727Leu missense_variant 1.0 ethambutol Uncertain significance
embA 4244723 p.Gln497His missense_variant 1.0 ethambutol Uncertain significance
aftB 4267979 c.858G>C synonymous_variant 1.0 ethambutol Uncertain significance