Run ID: SRR13837508
Sample name:
Date: 2024-10-03T16:14:47.733892
Number of reads: 587580
Percentage reads mapped: 97.0
Median coverage: 20.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
| 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 | katG | p.Gly234Glu | Uncertain significance | Mutation from literature |
| 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 | 2155411 | p.Gly234Glu | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| Rv0010c | 13524 | p.Gly12Ala | missense_variant | 1.0 | isoniazid | |
| mshA | 576259 | c.912C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| ethionamide | Not assoc w R - Interim | |||||
| ccsA | 620690 | p.Val267Glu | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| Rv0565c | 657622 | c.-152G>A | upstream_gene_variant | 1.0 | ethionamide | |
| mmaA3 | 738209 | c.-60A>T | upstream_gene_variant | 1.0 | isoniazid | |
| rpoB | 759805 | c.-2T>C | upstream_gene_variant | 1.0 | rifampicin | |
| rpoB | 761961 | p.Pro719Thr | missense_variant | 1.0 | rifampicin | |
| rpoC | 764895 | p.Ile509Thr | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777574 | p.Phe303Leu | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 777578 | c.903C>G | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| mmpL5 | 778982 | c.-502A>C | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rplC | 801169 | p.Lys121* | stop_gained | 1.0 | linezolid | |
| rrl | 1474052 | n.395G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476479 | n.2822T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| tlyA | 1918432 | p.Pro165Thr | missense_variant | 1.0 | capreomycin | |
| ndh | 2101769 | p.Arg425His | missense_variant | 1.0 | isoniazid | Uncertain significance |
| delamanid | ||||||
| ethionamide | ||||||
| katG | 2155508 | p.Ala202Ser | missense_variant | 1.0 | isoniazid | Uncertain significance |
| pncA | 2289474 | c.-233C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| folC | 2746862 | p.Leu246Arg | missense_variant | 0.97 | para-aminosalicylic_acid | |
| folC | 2747268 | p.Asp111His | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2752c | 3065109 | c.1083A>G | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| whiB7 | 3568816 | c.-137C>T | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| whiB7 | 3569222 | c.-543G>A | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| lpqB | 3624508 | p.Ile135Val | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3625247 | p.Arg456Pro | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| clpC1 | 4038468 | p.Asp746Gly | missense_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040148 | p.Lys186Ile | missense_variant | 1.0 | pyrazinamide | |
| embC | 4240125 | p.Cys88Tyr | missense_variant | 1.0 | ethambutol | |
| ethR | 4327643 | p.Thr32Ile | missense_variant | 1.0 | ethionamide |
