Run ID: SRR29096420
Sample name:
Date: 2024-09-26T22:18:02.495819
Number of reads: 33864
Percentage reads mapped: 43.17
Median coverage: 0.0
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 | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | fgd1 | c.838_840delATCinsGG | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fgd1 | 491620 | c.838_840delATCinsGG | frameshift_variant&missense_variant | 0.87 | pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| fgd1 | 491523 | c.741G>C | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491526 | c.744T>C | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491542 | c.760T>C | synonymous_variant | 0.91 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491547 | c.765A>G | synonymous_variant | 0.92 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491563 | c.781_783delAGCinsTCG | synonymous_variant | 0.92 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491595 | c.813C>T | synonymous_variant | 0.95 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491610 | c.828A>G | synonymous_variant | 0.89 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491616 | c.834A>G | synonymous_variant | 0.88 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491649 | c.867C>T | synonymous_variant | 0.83 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491655 | c.873C>T | synonymous_variant | 0.82 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491658 | c.876A>G | synonymous_variant | 0.82 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491661 | c.879C>G | synonymous_variant | 0.82 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491667 | c.885A>G | synonymous_variant | 0.8 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491676 | c.894T>C | synonymous_variant | 0.8 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fgd1 | 491679 | c.897A>G | synonymous_variant | 0.8 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoB | 760082 | c.276C>T | synonymous_variant | 0.9 | rifampicin | Not assoc w R - Interim |
| rpoB | 760088 | c.282C>G | synonymous_variant | 0.9 | rifampicin | |
| rpoB | 760091 | c.285G>C | synonymous_variant | 0.9 | rifampicin | Not assoc w R - Interim |
| rpoB | 760101 | c.295T>C | synonymous_variant | 0.9 | rifampicin | Not assoc w R - Interim |
| rpoB | 760104 | c.298_300delTCGinsAGC | synonymous_variant | 0.9 | rifampicin | |
| rpoB | 760112 | c.306T>C | synonymous_variant | 0.91 | rifampicin | |
| rpoB | 760118 | c.312T>G | synonymous_variant | 0.91 | rifampicin | Not assoc w R - Interim |
| rpoB | 760121 | c.315T>C | synonymous_variant | 0.92 | rifampicin | Not assoc w R - Interim |
| rpoB | 760130 | p.Asp108Glu | missense_variant | 0.93 | rifampicin | Uncertain significance |
| rpoB | 760136 | c.330G>A | synonymous_variant | 0.93 | rifampicin | |
| rpoB | 760139 | c.333A>T | synonymous_variant | 0.94 | rifampicin | |
| rpoB | 760142 | c.336C>G | synonymous_variant | 0.94 | rifampicin | |
| rpoB | 760178 | c.372G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 760181 | c.375T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 760184 | c.378A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 760196 | c.390C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 760235 | c.429T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 760244 | c.438G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 760283 | c.477G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| clpC1 | 4038623 | c.2082A>G | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038640 | p.Asp689Asn | missense_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038647 | c.2058T>G | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038658 | p.Lys683Gln | missense_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038660 | c.2044_2045delTCinsAG | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038662 | c.2043T>C | synonymous_variant | 1.0 | pyrazinamide | |
| clpC1 | 4038671 | c.2034T>G | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| clpC1 | 4038683 | c.2022T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
