Run ID: ERR2791539
Sample name:
Date: 2024-10-04T19:01:40.037389
Number of reads: 2723472
Percentage reads mapped: 99.61
Median coverage: 94.0
Strain: lineage4.6
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | 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 |
|---|---|---|---|---|---|---|
| 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13638 | c.-80A>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| ccsA | 620039 | p.Pro50Leu | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| mmaA3 | 738071 | p.Ala27Thr | missense_variant | 1.0 | isoniazid | |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 778693 | c.-213C>T | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1258c | 1406504 | c.837C>T | synonymous_variant | 1.0 | streptomycin | |
| pyrazinamide | Not assoc w R - Interim | |||||
| isoniazid | Not assoc w R - Interim | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| 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 |
| tlyA | 1918690 | p.Leu251Val | missense_variant | 1.0 | capreomycin | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| ahpC | 2726043 | c.-150C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2681 | 2997666 | p.Val310Met | missense_variant | 1.0 | capreomycin | |
| Rv3083 | 3449722 | p.Cys407Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269630 | c.204G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338593 | c.-72C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407691 | p.Val171Ala | missense_variant | 1.0 | streptomycin | |
| gid | 4407948 | p.Asp85Glu | missense_variant | 1.0 | streptomycin | Uncertain significance |
