Run ID: ERR11081199
Sample name:
Date: 2024-04-15T13:16:20.139643
Number of reads: 3816746
Percentage reads mapped: 99.69
Median coverage: 122.0
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 | |||||
| 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 |
| fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| 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 |
| PPE35 | 2169041 | c.1572G>A | synonymous_variant | 0.33 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2169044 | c.1569G>C | synonymous_variant | 0.46 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2169047 | c.1564_1566delATCinsGT | frameshift_variant&missense_variant | 0.42 | pyrazinamide | Uncertain significance |
| PPE35 | 2169053 | c.1560T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2169056 | c.1557A>G | synonymous_variant | 0.42 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2169059 | c.1554G>A | synonymous_variant | 0.58 | pyrazinamide | |
| PPE35 | 2169063 | p.Met517Thr | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2169065 | p.Ala516Ile | missense_variant | 0.58 | pyrazinamide | |
| PPE35 | 2169068 | c.1545G>T | synonymous_variant | 0.62 | pyrazinamide | |
| PPE35 | 2169071 | c.1542A>G | synonymous_variant | 0.33 | pyrazinamide | Not assoc w R - Interim |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| 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 | 4338614 | c.-93G>C | upstream_gene_variant | 0.99 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| whiB6 | 4338809 | c.-288A>G | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
