Run ID: ERR6397175
Sample name:
Date: 2024-04-15T07:12:13.119035
Number of reads: 6168177
Percentage reads mapped: 99.71
Median coverage: 107.0
Strain: lineage4.3.3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.3 | Euro-American (LAM) | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.3.3 | Euro-American (LAM) | RD115 | 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 | 536 | p.Ile179Thr | 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 | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8040 | p.Gly247Ser | 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 | |||||
| rpoB | 761196 | c.1390C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| 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 |
| fbiC | 1304565 | c.1635C>T | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rpsA | 1833483 | c.-59G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| 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 |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.4 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.4 | pyrazinamide | |
| PPE35 | 2170359 | p.Gln85Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 | isoniazid | |
| Rv2752c | 3067014 | c.-823G>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3449388 | c.885G>A | synonymous_variant | 1.0 | ethionamide | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3625421 | p.Asp398Gly | missense_variant | 1.0 | bedaquiline | |
| rifampicin | Uncertain significance | |||||
| fbiA | 3640394 | c.-149G>A | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4245945 | p.Ile905Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.2 | ethambutol | Uncertain significance |
| embB | 4246548 | p.Pro12Gln | missense_variant | 0.19 | ethambutol | Uncertain significance |
| embB | 4246555 | c.42G>C | synonymous_variant | 0.18 | ethambutol | |
| embB | 4246556 | p.Ala15Pro | missense_variant | 0.17 | ethambutol | Uncertain significance |
| embB | 4246563 | p.Leu17Trp | missense_variant | 0.18 | ethambutol | Uncertain significance |
| embB | 4246567 | c.54G>T | synonymous_variant | 0.19 | ethambutol | Not assoc w R - Interim |
| ethA | 4326570 | p.Phe302Leu | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338307 | p.Ala72Glu | missense_variant | 1.0 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| 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 | ||||||
| gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |
