Run ID: SRR13837564
Sample name:
Date: 2024-04-15T19:49:27.190467
Number of reads: 588748
Percentage reads mapped: 97.19
Median coverage: 20.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| 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 | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 7837 | p.Gly179Val | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| rpoB | 762257 | c.2451C>G | synonymous_variant | 1.0 | rifampicin | |
| mmpL5 | 777730 | p.Gly251Arg | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| fbiC | 1304816 | p.His629Arg | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1304869 | p.Leu647Met | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| sigE | 1364580 | p.Asp56Glu | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1917613 | c.-327G>T | upstream_gene_variant | 1.0 | capreomycin | |
| tlyA | 1918527 | c.588G>T | synonymous_variant | 1.0 | capreomycin | |
| bacA | 2064771 | c.-44delG | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| ndh | 2102259 | p.Ser262Ala | missense_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| ndh | 2102557 | c.485delG | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| katG | 2156260 | c.-149C>A | upstream_gene_variant | 1.0 | isoniazid | |
| PPE35 | 2169123 | p.Thr497Ile | missense_variant | 1.0 | pyrazinamide | |
| Rv2681 | 2997346 | c.609dupG | frameshift_variant | 1.0 | capreomycin | Uncertain significance |
| Rv2752c | 3066145 | p.Leu16Ser | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv3236c | 3612326 | p.Thr264Ile | missense_variant | 1.0 | pyrazinamide | |
| Rv3236c | 3612504 | p.His205Tyr | missense_variant | 1.0 | pyrazinamide | |
| Rv3236c | 3612779 | p.Leu113* | stop_gained | 1.0 | pyrazinamide | Uncertain significance |
| lpqB | 3623745 | p.Asp389Gly | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| lpqB | 3624635 | c.275_276insT | frameshift_variant | 1.0 | bedaquiline | |
| rifampicin | Uncertain significance | |||||
| fbiB | 3640821 | c.-714G>C | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoA | 3878381 | p.Leu43Met | missense_variant | 1.0 | rifampicin | |
| rpoA | 3878543 | c.-36G>C | upstream_gene_variant | 1.0 | rifampicin | |
| embC | 4239354 | c.-509A>T | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4240536 | c.678delC | frameshift_variant | 1.0 | ethambutol | |
| embB | 4248562 | c.2049G>C | synonymous_variant | 1.0 | ethambutol |
