Run ID: SRR5341219
Sample name:
Date: 2024-10-05T09:08:51.767651
Number of reads: 498602
Percentage reads mapped: 99.45
Median coverage: 14.0
Strain: lineage3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage3 | East-African-Indian | RD750 | 0.62 |
| 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 | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8948 | c.1647G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| tlyA | 1918335 | p.Glu132Asp | missense_variant | 1.0 | capreomycin | |
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| panD | 4044872 | c.-591C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4139275 | p.Gly161Arg | missense_variant | 0.46 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4328067 | c.-594T>G | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338604 | c.-83G>A | upstream_gene_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | ||||||
| amikacin | ||||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
