Run ID: ERR11049430
Sample name:
Date: 2024-04-15T17:59:17.065990
Number of reads: 5713355
Percentage reads mapped: 99.54
Median coverage: 177.0
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 |
|---|---|---|---|---|---|---|
| gyrB | 5578 | c.339G>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| 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 | 9171 | p.Val624Leu | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474669 | n.1015delC | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| tsnR | 1854241 | c.636C>G | synonymous_variant | 1.0 | linezolid | Not assoc w R - Interim |
| 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 |
| katG | 2154915 | c.1197A>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| PPE35 | 2169383 | c.1230C>G | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2170685 | c.-73C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2680 | 2995929 | c.-176C>T | upstream_gene_variant | 1.0 | capreomycin | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| whiB7 | 3569092 | c.-413C>T | upstream_gene_variant | 1.0 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiA | 3640308 | c.-235C>T | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiA | 3640347 | c.-196A>C | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4328320 | c.-847C>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 | ||||||
| gid | 4408358 | c.-156C>G | upstream_gene_variant | 1.0 | streptomycin |
