Run ID: SRR13837949
Sample name:
Date: 2024-10-05T06:18:46.390028
Number of reads: 1481438
Percentage reads mapped: 97.81
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 |
|---|---|---|---|---|---|---|
| gyrB | 6715 | c.1476C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | Not assoc w R - Interim | |||||
| mshA | 575693 | p.Pro116Ala | missense_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| nusG | 734493 | p.Phe80Leu | missense_variant | 0.98 | rifampicin | |
| rpoB | 759863 | p.Gln19His | missense_variant | 1.0 | rifampicin | |
| rpoB | 760399 | p.Val198Ala | missense_variant | 0.97 | rifampicin | |
| rpoB | 763150 | p.Phe1115Tyr | missense_variant | 1.0 | rifampicin | |
| rpoC | 764516 | p.Asp383Asn | missense_variant | 0.98 | rifampicin | |
| rpoC | 766103 | p.Arg912Gly | missense_variant | 1.0 | rifampicin | |
| mmpL5 | 777066 | p.Ile472Ser | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781333 | c.-227C>G | upstream_gene_variant | 1.0 | streptomycin | |
| embR | 1417750 | c.-403G>C | upstream_gene_variant | 1.0 | ethambutol | |
| bacA | 2063818 | c.910delC | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| ndh | 2103185 | c.-143A>C | upstream_gene_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2168894 | c.1718dupG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170039 | p.Ala192Thr | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2221777 | p.Ala463Val | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| kasA | 2518793 | p.Ser227Thr | missense_variant | 1.0 | isoniazid | |
| ahpC | 2726300 | c.108C>A | synonymous_variant | 1.0 | isoniazid | |
| folC | 2747094 | p.Asp169His | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2752c | 3064936 | p.Ser419* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| Rv2752c | 3065523 | c.669C>T | synonymous_variant | 0.98 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv2752c | 3066039 | c.153C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| lpqB | 3623677 | p.Val412Phe | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| alr | 3841286 | c.135T>A | synonymous_variant | 1.0 | cycloserine | |
| clpC1 | 4039368 | p.Lys446Thr | missense_variant | 1.0 | pyrazinamide | |
| embC | 4241777 | p.Gly639Ser | missense_variant | 1.0 | ethambutol | |
| ubiA | 4269888 | c.-55C>A | upstream_gene_variant | 1.0 | ethambutol |
