TB-Profiler result

Run: SRR13837975
Summary

Run ID: SRR13837975

Sample name:

Date: 2025-03-05T04:13:11.186174

Number of reads: 2936734

Percentage reads mapped: 100.0

Median coverage: 99.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 embC p.Tyr296His Mutation from literature
embB p.Met482Ile Mutation from literature
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 p.Tyr26* Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 p.Tyr26* Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
mmpR5 779067 p.Tyr26* stop_gained 1.0 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
embC 4240748 p.Tyr296His missense_variant 1.0 ethambutol Mutation from literature
embB 4247959 p.Met482Ile missense_variant 0.99 ethambutol Mutation from literature
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
fgd1 491360 p.Ile193Ser missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 576396 p.Ser350Ile missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoB 760225 p.Glu140Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 767186 p.Gln1273* stop_gained 1.0 rifampicin Uncertain significance
rplC 800933 p.Pro42His missense_variant 1.0 linezolid Uncertain significance
fbiC 1305306 c.2376A>T synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
tlyA 1918560 c.621G>T synonymous_variant 1.0 capreomycin Uncertain significance
bacA 2063120 c.1609C>T synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Not assoc w R - Interim
ndh 2102402 p.Leu214Arg missense_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2156175 c.-64T>G upstream_gene_variant 0.99 isoniazid Uncertain significance
PPE35 2169349 p.Phe422Ile missense_variant 0.99 pyrazinamide Uncertain significance
PPE35 2170540 p.Leu25Val missense_variant 1.0 pyrazinamide Uncertain significance
pncA 2288999 p.Phe81Leu missense_variant 1.0 pyrazinamide Uncertain significance
fbiD 3339660 c.543C>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv3236c 3612627 p.Ala164Thr missense_variant 1.0 pyrazinamide Uncertain significance
fbiA 3640219 c.-324C>T upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embA 4244119 p.Tyr296Phe missense_variant 1.0 ethambutol Uncertain significance
embB 4247417 p.Tyr302Asn missense_variant 1.0 ethambutol Uncertain significance
embB 4248036 p.Val508Gly missense_variant 1.0 ethambutol Uncertain significance
embB 4248325 c.1812G>C synonymous_variant 1.0 ethambutol Uncertain significance
aftB 4267894 p.Ile315Phe missense_variant 1.0 ethambutol Uncertain significance
ethA 4326052 p.Asp474Glu missense_variant 1.0 ethionamide Uncertain significance
ethA 4327388 p.Thr29Ile missense_variant 0.99 ethionamide Uncertain significance
ethR 4328162 p.His205Pro missense_variant 0.99 ethionamide Uncertain significance
whiB6 4338518 c.4C>A synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance