Run ID: SRR9166035
Sample name:
Date: 2024-03-26T19:54:01.801656
Number of reads: 12627084
Percentage reads mapped: 99.81
Median coverage: 206.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | fgd1 | c.412dupC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
fgd1 | 491193 | c.412dupC | frameshift_variant | 0.98 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.97 | isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.31 | pyrazinamide | |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.29 | pyrazinamide | |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.16 | ethambutol | Uncertain significance |
embB | 4246555 | c.42G>C | synonymous_variant | 0.22 | ethambutol | |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.23 | ethambutol | Uncertain significance |