TB-Profiler result

Run: ERR1035296
Summary

Run ID: ERR1035296

Sample name:

Date: 2025-03-08T10:02:55.405925

Number of reads: 10398945

Percentage reads mapped: 99.81

Median coverage: 187.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 katG c.316dupG Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA p.Ala171Val Uncertain significance Mutation from literature
c.246delT Assoc w R
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
katG 2155795 c.316dupG frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288730 p.Ala171Val missense_variant 0.53 pyrazinamide Uncertain significance Mutation from literature
pncA 2288995 c.246delT frameshift_variant 0.38 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.99 isoniazid Uncertain significance 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656195 p.Gly426Cys missense_variant 1.0 ethionamide Uncertain significance
fbiC 1303257 c.327C>T synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
glpK 4138415 c.1341G>T synonymous_variant 0.99 ethambutol Not assoc w R - Interim
isoniazid Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R