TB-Profiler result

Run: ERR5979567
Summary

Run ID: ERR5979567

Sample name:

Date: 2024-10-05T10:05:05.501271

Number of reads: 7344370

Percentage reads mapped: 99.95

Median coverage: 237.0

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
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.363delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198delG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.363delG 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 779181 c.198delG frameshift_variant 0.16 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
mmpR5 779348 c.363delG frameshift_variant 0.14 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
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
mshA 576108 p.Ala254Gly missense_variant 0.26 isoniazid
ethionamide
mmpR5 779210 p.Leu74Pro missense_variant 0.12 bedaquiline
clofazimine
mmpR5 779285 p.Ala99Val missense_variant 0.13 bedaquiline
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin