TB-Profiler result

Run: SRR8589330
Summary

Run ID: SRR8589330

Sample name:

Date: 2024-04-15T15:29:35.705643

Number of reads: 1652718

Percentage reads mapped: 99.91

Median coverage: 84.0

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 pncA p.Gly132Ser Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 p.Cys46Arg Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 p.Cys46Arg Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. 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 779125 p.Cys46Arg missense_variant 0.12 clofazimine Assoc w R - Interim Can only confer resistance if genetically linked to a functional MmpL5
bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV. Can only confer resistance if genetically linked to a functional MmpL5
pncA 2288848 p.Gly132Ser missense_variant 0.99 pyrazinamide Assoc w R
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
mmpR5 779095 p.Ala36Thr missense_variant 0.16 clofazimine
bedaquiline
mmpR5 779146 p.Ser53Pro missense_variant 0.24 clofazimine Uncertain significance
bedaquiline Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
glpK 4139568 p.Ile63Thr missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid