Run ID: ERR550632
Sample name:
Date: 2025-04-30T12:37:52.207648
Number of reads: 4120747
Percentage reads mapped: 99.68
Median coverage: 83.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 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 | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| 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 | amikacin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| 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 | 0.55 | pyrazinamide | Uncertain significance |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.55 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pepQ | 2860617 | c.-199C>T | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
| Rv3083 | 3448507 | c.5_*1407del | frameshift_variant&stop_lost&splice_region_variant | 0.99 | ethionamide | Uncertain significance |
| Rv3236c | 3612047 | p.Ala357Val | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.27 | ethambutol | Uncertain significance |
| embB | 4246548 | p.Pro12Gln | missense_variant | 0.36 | ethambutol | Uncertain significance |
| embB | 4246555 | c.42G>C | synonymous_variant | 0.36 | ethambutol | Uncertain significance |
| embB | 4246556 | p.Ala15Pro | missense_variant | 0.36 | ethambutol | Uncertain significance |
| embB | 4246563 | p.Leu17Trp | missense_variant | 0.24 | ethambutol | Uncertain significance |
| embB | 4246567 | c.54G>T | synonymous_variant | 0.21 | ethambutol | Not assoc w R - Interim |
| embB | 4246820 | p.Pro103Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ethA | 4326505 | c.969C>G | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | amikacin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| kanamycin | Not assoc w R |
