Run ID: SRR13837494
Sample name:
Date: 2024-04-15T22:29:06.614871
Number of reads: 590932
Percentage reads mapped: 95.53
Median coverage: 20.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | ethA | p.Trp45* | Assoc w R | |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| ethA | 4327340 | p.Trp45* | stop_gained | 1.0 | ethionamide | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 8646 | p.Gln449Lys | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9138 | p.Gln613Lys | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9604 | p.Val768Ala | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| Rv0010c | 13326 | c.232delC | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
| ccsA | 619641 | c.-250T>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| ccsA | 620748 | c.858T>G | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| Rv0565c | 656228 | p.Ala415Ser | missense_variant | 1.0 | ethionamide | |
| rpoB | 761853 | p.Ile683Val | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777509 | c.972G>T | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| mmpS5 | 779508 | c.-603G>C | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv1258c | 1406904 | c.436dupT | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
| isoniazid | Uncertain significance | |||||
| pyrazinamide | Uncertain significance | |||||
| Rv1258c | 1407127 | p.Arg72Ser | missense_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrs | 1472973 | n.1128A>G | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| inhA | 1674552 | c.351C>G | synonymous_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpsA | 1834079 | p.Arg180Cys | missense_variant | 1.0 | pyrazinamide | |
| bacA | 2063798 | p.Thr311Ser | missense_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| PPE35 | 2168448 | p.Gln722Pro | missense_variant | 0.96 | pyrazinamide | |
| Rv1979c | 2221876 | p.Val430Glu | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| kasA | 2518036 | c.-78delG | upstream_gene_variant | 1.0 | isoniazid | |
| kasA | 2518088 | c.-27T>A | upstream_gene_variant | 1.0 | isoniazid | |
| eis | 2714449 | p.Trp295Ser | missense_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| eis | 2714773 | p.Pro187Gln | missense_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| eis | 2715525 | c.-193G>T | upstream_gene_variant | 1.0 | amikacin | |
| kanamycin | ||||||
| ahpC | 2726611 | c.419_420insA | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
| folC | 2747455 | c.144C>A | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
| pepQ | 2859723 | c.696T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| bedaquiline | ||||||
| ribD | 2987540 | c.702G>T | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3339321 | c.204G>A | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| clpC1 | 4038436 | p.Ala757Ser | missense_variant | 1.0 | pyrazinamide | |
| embC | 4239186 | c.-677A>C | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4242635 | p.Ala925Ser | missense_variant | 1.0 | ethambutol | |
| embB | 4249145 | c.2634delC | frameshift_variant | 1.0 | ethambutol | |
| ubiA | 4269803 | p.Ala11Pro | missense_variant | 1.0 | ethambutol | |
| ethA | 4326689 | p.Lys262Thr | missense_variant | 1.0 | ethionamide | |
| ethA | 4326849 | p.Pro209Thr | missense_variant | 1.0 | ethionamide | |
| whiB6 | 4338822 | c.-301A>C | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
