Run ID: ERR10465796
Sample name:
Date: 2024-04-15T18:15:49.098162
Number of reads: 6219287
Percentage reads mapped: 99.67
Median coverage: 192.0
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 | 427 | p.Asn143Asp | missense_variant | 1.0 | isoniazid | Uncertain significance |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.35 | ethionamide | |
| isoniazid | ||||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 775715 | c.2766G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpS5 | 779611 | c.-706G>A | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| ndh | 2102006 | p.Thr346Met | missense_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | ||||||
| isoniazid | Uncertain significance | |||||
| katG | 2156703 | c.-592C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| eis | 2715101 | p.Pro78Ser | missense_variant | 1.0 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| Rv2752c | 3066939 | c.-748C>T | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv3083 | 3447873 | c.-630_*9806del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247028 | p.Leu172Arg | missense_variant | 0.2 | ethambutol | |
| embB | 4248487 | c.1974C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| 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 | |||||
| gid | 4407590 | p.Ala205Thr | missense_variant | 1.0 | streptomycin | Uncertain significance |
