Run ID: ERR439942
Sample name:
Date: 2024-05-17T14:18:18.627019
Number of reads: 3520545
Percentage reads mapped: 99.52
Median coverage: 73.0
Strain: lineage4.6.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.77 |
| 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 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| gyrA | 7539 | p.Thr80Ala | missense_variant | 1.0 | moxifloxacin | Not assoc w R - Interim |
| levofloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| gyrA | 8717 | c.1416C>T | synonymous_variant | 0.85 | moxifloxacin | |
| levofloxacin | Not assoc w R - Interim | |||||
| gyrA | 8774 | c.1473C>A | synonymous_variant | 0.9 | moxifloxacin | |
| levofloxacin | Not assoc w R - Interim | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rpoC | 764810 | p.Pro481Thr | missense_variant | 0.15 | rifampicin | Uncertain significance |
| 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 |
| Rv1129c | 1254580 | c.-46C>G | upstream_gene_variant | 0.92 | isoniazid | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| levofloxacin | Uncertain significance | |||||
| embR | 1416410 | p.Leu313Arg | missense_variant | 0.14 | ethambutol | Uncertain significance |
| embR | 1417040 | p.Leu103Arg | missense_variant | 0.93 | ethambutol | Uncertain significance |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| capreomycin | ||||||
| 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 |
| Rv1979c | 2221767 | p.His466Gln | missense_variant | 0.93 | clofazimine | |
| bedaquiline | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2681 | 2996876 | c.138A>C | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Not assoc w R | |||||
| panD | 4044842 | c.-561G>A | upstream_gene_variant | 0.83 | pyrazinamide | |
| glpK | 4139670 | p.Cys29Tyr | missense_variant | 1.0 | isoniazid | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| levofloxacin | Not assoc w R | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338391 | p.Thr44Ile | missense_variant | 0.88 | 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 | 0.99 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407555 | c.648A>G | synonymous_variant | 0.92 | streptomycin | Not assoc w R - Interim |
| gid | 4407716 | p.Lys163Glu | missense_variant | 0.93 | streptomycin | Uncertain significance |
