Run ID: SRR13837683
Sample name:
Date: 2024-10-05T07:37:55.175607
Number of reads: 293886
Percentage reads mapped: 98.01
Median coverage: 10.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| 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 | ||||
| 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 |
|---|---|---|---|---|---|---|
| gyrB | 5192 | c.-48C>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9658 | c.2357_2358insT | frameshift_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0565c | 657379 | p.Arg31His | missense_variant | 1.0 | ethionamide | |
| rpoB | 760041 | p.Gly79Arg | missense_variant | 1.0 | rifampicin | |
| rrl | 1473740 | n.83G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| PPE35 | 2168706 | p.Ser636Phe | missense_variant | 1.0 | pyrazinamide | |
| Rv2477c | 2783316 | p.Thr243Ala | missense_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| ribD | 2987500 | p.Gly221Asp | missense_variant | 1.0 | para-aminosalicylic_acid | |
| thyX | 3068082 | c.-137T>C | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3338954 | c.-164A>G | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiD | 3339235 | p.Leu40Val | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiD | 3339406 | p.Thr97Ala | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mtrB | 3626461 | c.153A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| bedaquiline | ||||||
| mtrB | 3626554 | c.60A>T | synonymous_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrA | 3627267 | p.Glu28Val | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| glpK | 4139747 | p.Asp3Glu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embA | 4244833 | p.Val534Ala | missense_variant | 1.0 | ethambutol | |
| aftB | 4267994 | p.Met281Ile | missense_variant | 1.0 | ethambutol |
