Run ID: SRR28045013
Sample name:
Date: 2024-05-22T11:23:07.124650
Number of reads: 1366829
Percentage reads mapped: 99.52
Median coverage: 35.0
Strain: lineage4.4
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.4 | Euro-American | None | 0.99 |
| 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 | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| 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 | 2168814 | p.Thr600Asn | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2169225 | p.Pro463Arg | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2170558 | p.Ala19Pro | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| eis | 2714523 | p.His270Gln | missense_variant | 1.0 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| Rv2752c | 3066452 | c.-261T>G | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243324 | p.Val31Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4247548 | c.1035C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4268928 | c.906C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269375 | c.459G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4328458 | c.-985C>T | upstream_gene_variant | 1.0 | ethionamide | |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
