Run ID: ERR552069
Sample name:
Date: 2024-04-15T21:38:59.145454
Number of reads: 4601094
Percentage reads mapped: 99.74
Median coverage: 83.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.7 | Euro-American (mainly T) | None | 1.0 |
| lineage4 | Euro-American | 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 | 1126 | c.1126C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| gyrA | 7270 | c.-32C>T | upstream_gene_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mshA | 575689 | c.342G>T | synonymous_variant | 1.0 | ethionamide | |
| isoniazid | Not assoc w R - Interim | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1258c | 1407604 | c.-264C>T | upstream_gene_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474294 | n.637C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1474452 | n.795C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.21 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.19 | pyrazinamide | |
| PPE35 | 2170675 | c.-63G>C | upstream_gene_variant | 0.99 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| eis | 2715432 | c.-100C>T | upstream_gene_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| pepQ | 2860298 | p.Gly41Cys | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| thyA | 3074589 | c.-118G>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| clpC1 | 4038258 | p.Ala816Val | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| embC | 4241611 | c.1749G>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4249732 | c.3219C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R |
