Run ID: SRR13837450
Sample name:
Date: 2024-04-15T07:52:23.338494
Number of reads: 881460
Percentage reads mapped: 100.0
Median coverage: 29.0
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 | 819 | c.819C>A | synonymous_variant | 1.0 | isoniazid | |
| gyrB | 5807 | p.Val190Phe | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 6898 | c.-404G>C | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8039 | c.738T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| mshA | 575293 | c.-55T>A | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| mshA | 575414 | p.Gly23Ser | missense_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| Rv0565c | 656618 | p.His285Asp | missense_variant | 1.0 | ethionamide | |
| rpoC | 765124 | c.1755G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| embR | 1417578 | c.-231T>C | upstream_gene_variant | 1.0 | ethambutol | |
| rpsA | 1834248 | p.His236Leu | missense_variant | 1.0 | pyrazinamide | |
| bacA | 2063871 | p.Phe286Leu | missense_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| katG | 2154449 | p.Ala555Ser | missense_variant | 1.0 | isoniazid | |
| PPE35 | 2170218 | p.Ala132Glu | missense_variant | 1.0 | pyrazinamide | |
| eis | 2715396 | c.-65delT | upstream_gene_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| ribD | 2987136 | p.Val100Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ribD | 2987590 | p.Leu251Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2681 | 2996731 | c.-8C>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv2752c | 3064996 | p.Thr399Asn | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| alr | 3841281 | p.His47Arg | missense_variant | 1.0 | cycloserine | |
| clpC1 | 4039292 | c.1413C>A | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4039426 | p.Lys427Gln | missense_variant | 1.0 | pyrazinamide | |
| embA | 4243228 | c.-5G>T | upstream_gene_variant | 0.97 | ethambutol | Uncertain significance |
| embA | 4243540 | p.Ala103Asp | missense_variant | 1.0 | ethambutol | |
| embA | 4244146 | p.Asp305Ala | missense_variant | 1.0 | ethambutol | |
| embB | 4249506 | c.2994delG | frameshift_variant | 1.0 | ethambutol |
