Run ID: ERR551867
Sample name:
Date: 2024-04-16T00:11:43.495079
Number of reads: 7905541
Percentage reads mapped: 99.68
Median coverage: 150.0
Strain: lineage4.6.2.2
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 1.0 |
| lineage4.6.2 | Euro-American | RD726 | 1.0 |
| lineage4.6.2.2 | Euro-American (Cameroon) | RD726 | 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 |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 778298 | c.183G>A | synonymous_variant | 0.99 | clofazimine | Not assoc w R - Interim |
| bedaquiline | Not assoc w R - Interim | |||||
| 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 | ||||||
| fabG1 | 1673346 | c.-94C>G | upstream_gene_variant | 0.11 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673349 | c.-91G>C | upstream_gene_variant | 0.11 | ethionamide | |
| isoniazid | ||||||
| fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.27 | ethionamide | |
| isoniazid | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2063187 | c.1542C>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| katG | 2155389 | c.723C>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.57 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.58 | pyrazinamide | |
| Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 0.92 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
| thyX | 3067474 | p.Pro158Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv3083 | 3448567 | p.His22Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3236c | 3612571 | c.546C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4242550 | c.2688C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.26 | ethambutol | Uncertain significance |
| embB | 4246548 | p.Pro12Gln | missense_variant | 0.29 | ethambutol | Uncertain significance |
| embB | 4246555 | c.42G>C | synonymous_variant | 0.29 | ethambutol | |
| embB | 4246556 | p.Ala15Pro | missense_variant | 0.29 | ethambutol | Uncertain significance |
| embB | 4246563 | p.Leu17Trp | missense_variant | 0.17 | ethambutol | Uncertain significance |
| embB | 4246567 | c.54G>T | synonymous_variant | 0.15 | ethambutol | Not assoc w R - Interim |
| aftB | 4267272 | p.Lys522Arg | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326739 | c.735C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethR | 4328004 | c.456G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
