Run ID: SRR16088026
Sample name:
Date: 2024-04-15T06:13:48.285159
Number of reads: 5565180
Percentage reads mapped: 99.65
Median coverage: 169.0
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 | |||||
| mshA | 576651 | p.Asp435Ala | missense_variant | 0.2 | ethionamide | |
| isoniazid | ||||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 775764 | p.Val906Ala | missense_variant | 0.99 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| fbiC | 1304155 | c.1225C>A | synonymous_variant | 0.99 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1416759 | c.589C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1473645 | n.-12delT | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| 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 |
| Rv1979c | 2222842 | c.322delG | frameshift_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2752c | 3067180 | c.-989C>A | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.32 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| whiB7 | 3568431 | c.249C>G | synonymous_variant | 0.26 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| lpqB | 3623610 | p.Ala434Val | missense_variant | 1.0 | bedaquiline | |
| rifampicin | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244637 | p.Val469Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embA | 4245835 | p.Leu868Arg | missense_variant | 0.17 | ethambutol | |
| ethA | 4328471 | c.-998A>G | 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 | |||||
| gid | 4407834 | p.Trp123Cys | missense_variant | 0.99 | streptomycin | Uncertain significance |
