Run ID: SRR13837535
Sample name:
Date: 2024-04-15T05:24:51.750107
Number of reads: 588938
Percentage reads mapped: 98.22
Median coverage: 19.0
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 |
|---|---|---|---|---|---|---|
| dnaA | 1168 | p.Ile390Leu | missense_variant | 1.0 | isoniazid | |
| gyrB | 5210 | c.-30C>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 490574 | c.-209G>C | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| ccsA | 620747 | p.Gly286Val | missense_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| mmpS5 | 778670 | p.Gln79Pro | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781927 | p.Lys123Met | missense_variant | 0.95 | streptomycin | |
| Rv1129c | 1253316 | p.Gly407Ser | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| fbiC | 1304806 | p.Pro626Thr | missense_variant | 0.95 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1417610 | c.-264_-263insA | upstream_gene_variant | 1.0 | ethambutol | |
| rpsA | 1834614 | p.Ile358Ser | missense_variant | 1.0 | pyrazinamide | |
| tsnR | 1853786 | c.181T>C | synonymous_variant | 1.0 | linezolid | |
| PPE35 | 2169834 | p.Gly260Val | missense_variant | 1.0 | pyrazinamide | |
| kasA | 2518887 | p.Gly258Val | missense_variant | 1.0 | isoniazid | |
| eis | 2715520 | c.-188C>T | upstream_gene_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| ahpC | 2725916 | c.-277_-276insA | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2477c | 2782523 | p.Thr507Met | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2782875 | p.Asp390His | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2784377 | c.-335T>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| pepQ | 2859750 | c.669C>T | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| lpqB | 3623317 | p.Gln532Glu | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| panD | 4044912 | c.-631T>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4139251 | p.Gly169Cys | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embA | 4245437 | p.Met735Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4246876 | c.363G>A | synonymous_variant | 1.0 | ethambutol | |
| embB | 4248914 | p.Ala801Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ubiA | 4269329 | p.Lys169Glu | missense_variant | 1.0 | ethambutol | |
| ethA | 4326973 | p.Trp167Cys | missense_variant | 1.0 | ethionamide | Uncertain significance |
| ethA | 4327382 | p.Ser31Ile | missense_variant | 1.0 | ethionamide |
