Run ID: SRR13837623
Sample name:
Date: 2024-04-15T00:41:16.855187
Number of reads: 2938202
Percentage reads mapped: 98.0
Median coverage: 99.0
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 | katG | c.926_927insA | Assoc w R | High-level resistance |
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2155185 | c.926_927insA | frameshift_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 8396 | p.Tyr365* | stop_gained | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13610 | c.-52A>C | upstream_gene_variant | 1.0 | isoniazid | |
| fgd1 | 490821 | p.Glu13Asp | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| mshA | 575959 | p.Gln204His | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpoC | 766364 | p.Ala999Ser | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 775945 | p.Val846Leu | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 778345 | p.Leu46Ile | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpL5 | 778992 | c.-512C>T | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpR5 | 779231 | p.Glu81Val | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 800526 | c.-283G>T | upstream_gene_variant | 1.0 | linezolid | |
| fbiC | 1303186 | p.Tyr86His | missense_variant | 0.98 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fabG1 | 1673157 | c.-283G>C | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| bacA | 2063272 | c.1456delC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| ndh | 2101749 | p.Thr432Ser | missense_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| katG | 2155982 | p.Asn44His | missense_variant | 1.0 | isoniazid | |
| PPE35 | 2168042 | c.2571G>C | synonymous_variant | 1.0 | pyrazinamide | |
| PPE35 | 2169365 | c.1248C>T | synonymous_variant | 1.0 | pyrazinamide | |
| Rv2477c | 2784596 | c.-554A>T | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| thyX | 3067878 | p.Val23Gly | missense_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3339188 | p.Thr24Ser | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| whiB7 | 3568496 | p.Pro62Ser | missense_variant | 0.99 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| Rv3236c | 3612323 | p.Pro265Gln | missense_variant | 1.0 | pyrazinamide | |
| fbiA | 3641121 | c.579C>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| pretomanid | ||||||
| delamanid | ||||||
| clpC1 | 4038346 | p.Glu787* | stop_gained | 1.0 | pyrazinamide | |
| glpK | 4139375 | p.Asp127Glu | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| glpK | 4139545 | p.Leu71Val | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4238896 | c.-967C>A | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4239894 | p.Ala11Gly | missense_variant | 1.0 | ethambutol | |
| ethA | 4327073 | p.Leu134Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
