Run ID: SRR13837997
Sample name:
Date: 2024-10-04T20:50:51.550230
Number of reads: 2986070
Percentage reads mapped: 96.55
Median coverage: 101.0
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 | pepQ | c.248_249insA | Assoc w R - Interim | |
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | pepQ | c.248_249insA | Assoc w R - Interim | Includes data from one site that only submitted resistant strains, which may have inflated the PPV |
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| pepQ | 2860170 | c.248_249insA | frameshift_variant | 1.0 | bedaquiline | Assoc w R - Interim | Includes data from one site that only submitted resistant strains, which may have inflated the PPV |
| clofazimine | Assoc w R - Interim |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 4992 | c.-248_-247insT | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7018 | c.-284G>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 576668 | c.1322dupA | frameshift_variant&stop_gained | 1.0 | isoniazid | Uncertain significance |
| ethionamide | Uncertain significance | |||||
| Rv0565c | 656976 | c.495G>A | synonymous_variant | 1.0 | ethionamide | |
| Rv0565c | 657336 | c.135G>C | synonymous_variant | 1.0 | ethionamide | |
| rpoC | 765100 | c.1731G>C | synonymous_variant | 0.97 | rifampicin | |
| mmpL5 | 776059 | p.Val808Met | missense_variant | 0.98 | bedaquiline | |
| clofazimine | ||||||
| fbiC | 1304599 | p.Ile557Phe | missense_variant | 0.97 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| embR | 1417348 | c.-1A>T | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1473631 | n.-27T>C | upstream_gene_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rpsA | 1833855 | p.Lys105Thr | missense_variant | 0.98 | pyrazinamide | |
| tlyA | 1917702 | c.-238G>C | upstream_gene_variant | 1.0 | capreomycin | |
| bacA | 2064233 | c.495dupG | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| katG | 2156789 | c.-678G>T | upstream_gene_variant | 1.0 | isoniazid | |
| PPE35 | 2170030 | p.Met195Leu | missense_variant | 1.0 | pyrazinamide | |
| kasA | 2518276 | p.Trp54* | stop_gained | 1.0 | isoniazid | |
| kasA | 2518352 | p.Met80Val | missense_variant | 1.0 | isoniazid | |
| eis | 2714478 | c.855C>A | synonymous_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| Rv2681 | 2997465 | p.Val243Leu | missense_variant | 1.0 | capreomycin | |
| Rv2752c | 3065335 | p.Leu286Arg | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| mtrB | 3626280 | p.Thr112Pro | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| fbiA | 3640236 | c.-307T>A | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiA | 3640307 | c.-236C>G | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3641019 | c.-516G>A | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3641941 | p.Leu136Gln | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| glpK | 4139862 | c.-107C>A | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embC | 4241292 | p.Leu477Gln | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4242011 | p.Leu717Val | missense_variant | 1.0 | ethambutol | |
| embB | 4248720 | p.Gly736Ala | missense_variant | 1.0 | ethambutol | |
| embB | 4249676 | p.Arg1055Cys | missense_variant | 1.0 | ethambutol | |
| aftB | 4267927 | p.Ala304Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
