Run ID: SRR10321152
Sample name:
Date: 2024-10-04T11:35:00.328768
Number of reads: 224943
Percentage reads mapped: 98.02
Median coverage: 7.0
Strain: La3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La3 | M.orygis | None | 0.33 |
| 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 | 5516 | p.Ile93Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrB | 6109 | c.870G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| gyrB | 6717 | p.Ile493Thr | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13315 | p.Ser82Pro | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13441 | p.Thr40Ala | missense_variant | 1.0 | isoniazid | Not assoc w R |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| rpsA | 1834363 | c.822G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2168054 | c.2559G>C | synonymous_variant | 1.0 | pyrazinamide | |
| PPE35 | 2169279 | c.1312_1333delAACAATGGTGTCTTTTACCGTG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170669 | c.-57G>A | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2289978 | c.-737T>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| ahpC | 2726378 | c.186T>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| folC | 2746391 | p.Val403Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| thyA | 3074494 | c.-81_-24delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| clpC1 | 4040945 | c.-241G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| ethA | 4328211 | c.-738A>G | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338269 | p.Gly85Ser | missense_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
