Run ID: SRR13837894
Sample name:
Date: 2024-10-05T02:16:50.533181
Number of reads: 1470772
Percentage reads mapped: 99.11
Median coverage: 49.0
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 |
|---|---|---|---|---|---|---|
| Rv0565c | 657052 | p.Phe140Cys | missense_variant | 1.0 | ethionamide | |
| sigE | 1364478 | c.66C>T | synonymous_variant | 1.0 | pyrazinamide | |
| rpsA | 1833851 | p.Lys104Gln | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223241 | c.-77C>G | upstream_gene_variant | 0.98 | bedaquiline | |
| clofazimine | ||||||
| pncA | 2289811 | c.-570C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| pncA | 2289994 | c.-753A>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518301 | p.His63Asp | missense_variant | 1.0 | isoniazid | |
| pepQ | 2859859 | p.Ala187Glu | missense_variant | 0.98 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| Rv2752c | 3064886 | p.Ala436Pro | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv2752c | 3065258 | p.Met312Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| Rv2752c | 3066561 | c.-370A>C | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv3083 | 3449104 | p.Pro201Ala | missense_variant | 1.0 | ethionamide | |
| Rv3236c | 3612337 | c.779delG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv3236c | 3613541 | c.-425C>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| mtrA | 3627882 | c.-533C>G | upstream_gene_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| fbiB | 3641723 | c.189T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rpoA | 3877740 | c.768G>T | synonymous_variant | 0.98 | rifampicin | |
| embC | 4239546 | c.-317C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4241005 | c.1143G>T | synonymous_variant | 1.0 | ethambutol | |
| embC | 4241081 | c.1220delT | frameshift_variant | 1.0 | ethambutol | |
| embC | 4242746 | p.Pro962Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4243969 | p.Val246Ala | missense_variant | 1.0 | ethambutol |
