Run ID: ERR11465954
Sample name:
Date: 2024-04-16T09:07:35.941827
Number of reads: 2566356
Percentage reads mapped: 99.74
Median coverage: 43.0
Strain: lineage4.8.1;lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 0.99 |
| lineage4.8 | Euro-American (mainly T) | RD219 | 0.85 |
| lineage4.8.1 | Euro-American (mainly T) | RD219 | 0.69 |
| lineage4.9 | Euro-American (H37Rv-like) | None | 0.05 |
| 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 | 0.91 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 0.17 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.23 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.16 | ethionamide | Not assoc w R - Interim |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.95 | 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 | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | Not assoc w R |
| linezolid | Not assoc w R | |||||
| rrl | 1476704 | n.3053delC | non_coding_transcript_exon_variant | 0.81 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.22 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 0.91 | capreomycin | Not assoc w R |
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.81 | pyrazinamide | Not assoc w R |
| PPE35 | 2170892 | c.-280G>A | upstream_gene_variant | 0.92 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.95 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv2477c | 2784617 | c.-575T>C | upstream_gene_variant | 0.8 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.65 | capreomycin | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.16 | cycloserine | |
| fbiD | 3339040 | c.-78T>C | upstream_gene_variant | 0.62 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiD | 3339113 | c.-5A>C | upstream_gene_variant | 0.61 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiB | 3642874 | p.Leu447Arg | missense_variant | 0.91 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| alr | 3840950 | p.Lys157Asn | missense_variant | 0.16 | cycloserine | |
| embC | 4242075 | p.Arg738Gln | missense_variant | 0.17 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 0.79 | ethambutol | Not assoc w R |
| embB | 4246544 | p.Thr11Pro | missense_variant | 0.42 | ethambutol | Uncertain significance |
| embB | 4246548 | p.Pro12Gln | missense_variant | 0.26 | ethambutol | Uncertain significance |
| embB | 4246555 | c.42G>C | synonymous_variant | 0.32 | ethambutol | |
| embB | 4246556 | p.Ala15Pro | missense_variant | 0.32 | ethambutol | Uncertain significance |
| embB | 4246563 | p.Leu17Trp | missense_variant | 0.31 | ethambutol | Uncertain significance |
| embB | 4246567 | c.54G>T | synonymous_variant | 0.32 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.96 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.14 | capreomycin | |
| amikacin | ||||||
| kanamycin |
