Run ID: SRR28860129
Sample name:
Date: 2025-02-11T10:53:18.084608
Number of reads: 4410010
Percentage reads mapped: 99.53
Median coverage: 137.0
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 |
|---|---|---|---|---|---|---|
| dnaA | 371 | p.Pro124Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 0.98 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mshA | 576651 | p.Asp435Ala | missense_variant | 0.18 | isoniazid | |
| ethionamide | ||||||
| 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 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| 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 |
| katG | 2155674 | c.438G>A | synonymous_variant | 1.0 | isoniazid | |
| PPE35 | 2169191 | c.1422G>T | synonymous_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv2477c | 2784217 | c.-212_-176delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC | upstream_gene_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2752c | 3066163 | p.Pro10Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv3083 | 3448500 | c.-3_*1407del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
| whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.23 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| alr | 3840764 | c.657G>C | synonymous_variant | 1.0 | cycloserine | |
| clpC1 | 4038764 | c.1941C>A | synonymous_variant | 1.0 | pyrazinamide | |
| embC | 4240413 | p.Leu184Arg | missense_variant | 0.21 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243662 | p.Asp144Asn | missense_variant | 1.0 | ethambutol | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R |
