Run ID: SRR13837954
Sample name:
Date: 2024-03-26T17:00:49.839461
Number of reads: 1469114
Percentage reads mapped: 97.0
Median coverage: 50.0
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 | 5624 | p.Asn129Asp | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 575194 | c.-154G>T | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| hadA | 731960 | p.His11Asp | missense_variant | 1.0 | isoniazid | |
| hadA | 732111 | p.Cys61Tyr | missense_variant | 1.0 | isoniazid | |
| rpoB | 760907 | c.1101_1102insT | frameshift_variant | 1.0 | rifampicin | |
| rplC | 801226 | p.Gly140Arg | missense_variant | 1.0 | linezolid | |
| Rv1129c | 1253913 | p.Ile208Phe | missense_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv1129c | 1254602 | c.-68C>T | upstream_gene_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| Rv1129c | 1254678 | c.-144A>G | upstream_gene_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| sigE | 1364750 | p.Thr113Ser | missense_variant | 1.0 | pyrazinamide | |
| embR | 1417503 | c.-156A>C | upstream_gene_variant | 1.0 | ethambutol | |
| embR | 1417613 | c.-266C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1476753 | n.3099delG | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| fabG1 | 1673233 | c.-207T>G | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpsA | 1833593 | c.53delC | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| rpsA | 1834884 | p.Gln448Leu | missense_variant | 1.0 | pyrazinamide | |
| bacA | 2064646 | p.Thr28Arg | missense_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| PPE35 | 2169282 | p.Arg444His | missense_variant | 1.0 | pyrazinamide | |
| ahpC | 2725932 | c.-261G>A | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2477c | 2783645 | p.Asp133Gly | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| pepQ | 2859739 | p.Ala227Gly | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| pepQ | 2860197 | c.222T>C | synonymous_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv2681 | 2997172 | p.Asp145Gly | missense_variant | 1.0 | capreomycin | |
| Rv3083 | 3448909 | p.Leu136Ile | missense_variant | 1.0 | ethionamide | |
| mtrA | 3627160 | p.Gly64Ser | missense_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| fbiA | 3640691 | p.Asp50Val | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiA | 3641204 | p.Gly221Asp | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoA | 3878967 | c.-460G>T | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4039961 | p.Tyr248* | stop_gained | 1.0 | pyrazinamide | |
| glpK | 4138333 | p.Ser475Pro | missense_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4240818 | p.Thr319Arg | missense_variant | 1.0 | ethambutol | |
| embB | 4248081 | c.1569dupG | frameshift_variant | 1.0 | ethambutol | |
| ethA | 4327644 | c.-171G>A | upstream_gene_variant | 1.0 | ethionamide |
