Run ID: SRR13837892
Sample name:
Date: 2024-10-04T11:43:30.349947
Number of reads: 1469078
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 |
|---|---|---|---|---|---|---|
| dnaA | 335 | p.Thr112Ser | missense_variant | 1.0 | isoniazid | |
| gyrB | 6406 | p.Asn389Lys | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 575880 | p.His178Pro | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| mshA | 576356 | p.Ala337Ser | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| mmaA3 | 738203 | c.-54T>C | upstream_gene_variant | 1.0 | isoniazid | |
| Rv1129c | 1254144 | p.Thr131Ala | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| fbiC | 1303517 | p.Met196Arg | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrl | 1473558 | n.-100T>G | upstream_gene_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| inhA | 1673792 | c.-410G>T | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| rpsA | 1833709 | c.168C>T | synonymous_variant | 1.0 | pyrazinamide | |
| rpsA | 1834448 | p.Lys303* | stop_gained | 1.0 | pyrazinamide | Uncertain significance |
| tlyA | 1917605 | c.-335G>T | upstream_gene_variant | 1.0 | capreomycin | |
| tlyA | 1918103 | p.Val55Ala | missense_variant | 1.0 | capreomycin | |
| tlyA | 1918250 | p.Gly104Ala | missense_variant | 1.0 | capreomycin | |
| bacA | 2064591 | c.138C>A | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| katG | 2156538 | c.-427A>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv1979c | 2222544 | c.621G>A | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| eis | 2715078 | c.255C>G | synonymous_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| folC | 2747750 | c.-152G>C | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2680 | 2995806 | c.-299_-298insC | upstream_gene_variant | 1.0 | capreomycin | |
| ald | 3086982 | p.Ala55Pro | missense_variant | 1.0 | cycloserine | |
| Rv3083 | 3449935 | p.Ile478Val | missense_variant | 1.0 | ethionamide | |
| whiB7 | 3569257 | c.-578A>G | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| lpqB | 3623916 | p.Arg332Gln | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3627581 | c.-968G>A | upstream_gene_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| fbiB | 3642147 | p.Val205Phe | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fbiB | 3642189 | p.Gly219Trp | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| clpC1 | 4039120 | p.Ser529Ala | missense_variant | 1.0 | pyrazinamide | |
| clpC1 | 4039306 | p.Gln467Lys | missense_variant | 1.0 | pyrazinamide | |
| clpC1 | 4039400 | c.1304delA | frameshift_variant | 1.0 | pyrazinamide | |
| embC | 4239311 | c.-552G>C | upstream_gene_variant | 1.0 | ethambutol | |
| ethA | 4327034 | p.Tyr147Phe | missense_variant | 1.0 | ethionamide | |
| gid | 4408038 | p.Ile55Met | missense_variant | 1.0 | streptomycin |
