Run ID: SRR3082138
Sample name:
Date: 2024-10-05T09:06:24.530682
Number of reads: 1395179
Percentage reads mapped: 99.47
Median coverage: 29.0
Strain: lineage4
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | 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 |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| ccsA | 620598 | c.708C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| capreomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| rpoB | 761889 | p.Val695Leu | missense_variant | 0.97 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 801009 | c.201A>G | synonymous_variant | 1.0 | linezolid | Not assoc w R - Interim |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.98 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476704 | n.3053delC | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2168280 | p.Pro778Leu | missense_variant | 0.96 | pyrazinamide | |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.55 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.55 | pyrazinamide | |
| Rv1979c | 2223214 | c.-50A>C | upstream_gene_variant | 0.98 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv2752c | 3065517 | c.675C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| isoniazid | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| ethambutol | Not assoc w R - Interim | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246782 | p.Ala90Gly | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ethA | 4327375 | c.99C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethA | 4328317 | c.-844C>T | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
