TB-Profiler result

Run: SRR13837657
Summary

Run ID: SRR13837657

Sample name:

Date: 2024-10-04T04:07:48.373320

Number of reads: 293862

Percentage reads mapped: 96.02

Median coverage: 10.0

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 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
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
ccsA 620144 c.255dupT frameshift_variant 1.0 kanamycin
capreomycin
amikacin
rpoB 760191 p.Val129Phe missense_variant 1.0 rifampicin
rpoB 760311 p.Val169Leu missense_variant 1.0 rifampicin
rpoC 763662 p.Ala98Asp missense_variant 1.0 rifampicin
mmpL5 777800 c.681C>T synonymous_variant 1.0 bedaquiline
clofazimine
fbiC 1304996 p.Leu689Ser missense_variant 0.94 pretomanid
delamanid
clofazimine
Rv1258c 1407148 p.Ala65Ser missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
embR 1416842 p.Asp169Gly missense_variant 1.0 ethambutol Uncertain significance
katG 2156606 c.-495T>C upstream_gene_variant 1.0 isoniazid
PPE35 2170268 c.345C>A synonymous_variant 1.0 pyrazinamide
kasA 2518311 p.Asp66Gly missense_variant 1.0 isoniazid
ahpC 2726589 p.Arg133Ser missense_variant 1.0 isoniazid
Rv2752c 3066289 c.-98T>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3087163 c.344_345insC frameshift_variant 1.0 cycloserine
Rv3236c 3612049 c.1068G>C synonymous_variant 1.0 pyrazinamide
Rv3236c 3612400 c.717G>A synonymous_variant 1.0 pyrazinamide
fbiB 3642445 p.Ala304Gly missense_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4040104 p.Met201Leu missense_variant 1.0 pyrazinamide
aftB 4268164 c.672_673insA frameshift_variant 1.0 ethambutol Uncertain significance