Run ID: ERR3276141
Sample name:
Date: 2024-10-04T23:04:30.837364
Number of reads: 4933952
Percentage reads mapped: 99.98
Median coverage: 69.0
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 |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7907 | p.Phe202Leu | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| mshA | 575891 | p.Ala182Thr | missense_variant | 1.0 | isoniazid | Uncertain significance |
| ethionamide | Uncertain significance | |||||
| Rv0565c | 656761 | p.Thr237Ile | missense_variant | 1.0 | ethionamide | 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 |
| embR | 1417866 | c.-519T>C | upstream_gene_variant | 1.0 | ethambutol | |
| 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 | |||||
| rrl | 1475484 | n.1827A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476329 | n.2672A>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.1 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| eis | 2714678 | p.His219Tyr | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| pepQ | 2859733 | p.Tyr229Cys | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| clpC1 | 4040853 | c.-149T>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040941 | c.-237G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247595 | p.Cys361Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R |
