Run ID: SRR27450192
Sample name:
Date: 2024-03-26T15:24:44.391457
Number of reads: 10073353
Percentage reads mapped: 98.83
Median coverage: 329.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | 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 | 8636 | c.1335A>G | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 576651 | p.Asp435Ala | missense_variant | 0.22 | ethionamide | |
| isoniazid | ||||||
| mshA | 576657 | p.Leu437Arg | missense_variant | 0.15 | ethionamide | |
| isoniazid | ||||||
| rpoC | 763061 | c.-309C>T | upstream_gene_variant | 0.99 | rifampicin | |
| rpoC | 766670 | p.Asp1101Asn | missense_variant | 1.0 | rifampicin | |
| 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 |
| 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 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2477c | 2782772 | p.Ala424Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| Rv2477c | 2784277 | c.-235C>A | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.18 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| glpK | 4139183 | c.572dupG | frameshift_variant | 0.2 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| glpK | 4139395 | p.Arg121Gly | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| whiB6 | 4338228 | c.294G>A | synonymous_variant | 0.99 | capreomycin | |
| amikacin | Not assoc w R - Interim | |||||
| kanamycin | 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 |
