TB-Profiler result

Run: SRR13861427
Summary

Run ID: SRR13861427

Sample name:

Date: 2024-04-15T19:49:54.089111

Number of reads: 1313088

Percentage reads mapped: 32.86

Median coverage: 45.0

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 1.0 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
pretomanid
delamanid
mshA 576396 p.Ser350Ile missense_variant 1.0 ethionamide
isoniazid
rpoB 760225 p.Glu140Ala missense_variant 1.0 rifampicin
rpoC 767186 p.Gln1273* stop_gained 1.0 rifampicin
rplC 800933 p.Pro42His missense_variant 1.0 linezolid
fbiC 1305306 c.2376A>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
tlyA 1918560 c.621G>T synonymous_variant 1.0 capreomycin
bacA 2063120 c.1609C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin
capreomycin
amikacin
ndh 2102402 p.Leu214Arg missense_variant 1.0 ethionamide
delamanid
isoniazid Uncertain significance
katG 2156175 c.-64T>G upstream_gene_variant 1.0 isoniazid
PPE35 2169349 p.Phe422Ile missense_variant 1.0 pyrazinamide
PPE35 2170540 p.Leu25Val missense_variant 1.0 pyrazinamide
pncA 2288999 p.Phe81Leu missense_variant 1.0 pyrazinamide
fbiD 3339660 c.543C>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
Rv3236c 3612627 p.Ala164Thr missense_variant 1.0 pyrazinamide
fbiA 3640219 c.-324C>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
embA 4244119 p.Tyr296Phe missense_variant 1.0 ethambutol
embB 4247417 p.Tyr302Asn missense_variant 1.0 ethambutol
embB 4248036 p.Val508Gly missense_variant 1.0 ethambutol
embB 4248325 c.1812G>C synonymous_variant 1.0 ethambutol
aftB 4267894 p.Ile315Phe missense_variant 1.0 ethambutol
ethA 4326052 p.Asp474Glu missense_variant 1.0 ethionamide
ethA 4327388 p.Thr29Ile missense_variant 1.0 ethionamide
ethR 4328162 p.His205Pro missense_variant 1.0 ethionamide
whiB6 4338518 c.4C>A synonymous_variant 1.0 capreomycin
amikacin
kanamycin