Run ID: SRR21277532
Sample name:
Date: 2024-04-14T03:36:41.906254
Number of reads: 26801869
Percentage reads mapped: 98.07
Median coverage: 866.5
Strain: lineage4.5
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.5 | Euro-American | RD122 | 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 | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
| amikacin | Not assoc w R - Interim | |||||
| kanamycin | Not assoc w R - Interim | |||||
| 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 | 1302841 | c.-90C>T | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 0.98 | capreomycin | Not assoc w R |
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | 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 | 2784617 | c.-575T>C | upstream_gene_variant | 0.73 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| pepQ | 2860129 | p.Phe97Ser | missense_variant | 0.98 | clofazimine | |
| bedaquiline | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoA | 3878803 | c.-296G>T | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| embA | 4242580 | c.-653G>C | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| 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 | 4408216 | c.-14C>G | upstream_gene_variant | 1.0 | streptomycin |
