Run ID: SRR28389894
Sample name:
Date: 2024-10-04T15:52:04.337362
Number of reads: 2161478
Percentage reads mapped: 99.58
Median coverage: 71.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 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 | 371 | p.Pro124Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9184 | p.Arg628Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| 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 |
| rrs | 1471579 | n.-267C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2168981 | c.1632A>G | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2168987 | p.Thr542Ala | missense_variant | 0.15 | pyrazinamide | Uncertain significance |
| PPE35 | 2168990 | c.1623T>G | synonymous_variant | 0.15 | pyrazinamide | |
| PPE35 | 2169122 | c.1491C>G | synonymous_variant | 0.15 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2169125 | p.Val496Ile | missense_variant | 0.14 | pyrazinamide | Uncertain significance |
| PPE35 | 2169134 | c.1479G>A | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2169141 | p.Thr491Met | missense_variant | 0.13 | pyrazinamide | Uncertain significance |
| PPE35 | 2169144 | p.Val490Ala | missense_variant | 0.13 | pyrazinamide | Uncertain significance |
| PPE35 | 2169149 | c.1464G>A | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3236c | 3613475 | c.-359T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| alr | 3840764 | c.657G>C | synonymous_variant | 1.0 | cycloserine | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethR | 4328030 | p.Ala161Gly | missense_variant | 0.13 | 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 | 4338599 | c.-78A>C | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | Uncertain significance |
