Run ID: SRR28860155
Sample name:
Date: 2024-10-03T21:27:41.084724
Number of reads: 3576919
Percentage reads mapped: 99.53
Median coverage: 112.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: HR-TB
| 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 | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| 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 |
|---|---|---|---|---|---|---|---|
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| 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 | 9329 | c.2028C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13638 | c.-80A>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| mshA | 576618 | p.His424Pro | missense_variant | 0.22 | isoniazid | |
| ethionamide | ||||||
| mshA | 576651 | p.Asp435Ala | missense_variant | 0.2 | isoniazid | |
| ethionamide | ||||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 778467 | p.Arg5Lys | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| 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 |
| PPE35 | 2169547 | p.His356Tyr | missense_variant | 0.99 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223085 | p.Ile27Lys | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 1.0 | capreomycin | |
| Rv3083 | 3448500 | c.-3_*1408del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
| whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.23 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| alr | 3841080 | p.His114Arg | missense_variant | 1.0 | cycloserine | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| gid | 4407945 | c.258C>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
