Run ID: SRR13837706
Sample name:
Date: 2024-10-04T22:11:14.769992
Number of reads: 293779
Percentage reads mapped: 98.01
Median coverage: 10.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | fbiC | c.1301delC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiC | 1304229 | c.1301delC | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 8880 | p.Lys527Gln | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| rpoB | 760972 | p.Arg389Leu | missense_variant | 1.0 | rifampicin | |
| rpoC | 765540 | p.Ala724Val | missense_variant | 1.0 | rifampicin | |
| rpoC | 767068 | c.3699G>T | synonymous_variant | 1.0 | rifampicin | |
| rplC | 801357 | p.His183Gln | missense_variant | 1.0 | linezolid | |
| tlyA | 1917989 | p.Ala17Gly | missense_variant | 1.0 | capreomycin | |
| bacA | 2063805 | c.924G>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| bacA | 2064585 | c.144C>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| ndh | 2102525 | p.Phe173Tyr | missense_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| Rv1979c | 2222978 | p.Ile63Phe | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223052 | p.Glu38Val | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| eis | 2714983 | p.Ala117Glu | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| Rv2477c | 2784611 | c.-569A>T | upstream_gene_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| fbiA | 3640404 | c.-139C>A | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3642056 | c.522C>G | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| clpC1 | 4039777 | c.927_928insG | frameshift_variant | 1.0 | pyrazinamide | |
| aftB | 4268812 | p.Ser9Pro | missense_variant | 1.0 | ethambutol |
