Run ID: ERR4820979
Sample name:
Date: 2024-04-16T00:07:06.110025
Number of reads: 407020
Percentage reads mapped: 98.12
Median coverage: 9.0
Strain: lineage3;lineage4
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage3 | East-African-Indian | RD750 | 1.0 |
| lineage4 | Euro-American | None | 0.46 |
| 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 | |||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 766678 | c.3309C>T | synonymous_variant | 0.8 | rifampicin | Not assoc w R - Interim |
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.92 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| fbiC | 1303612 | p.Leu228Phe | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| sigE | 1364336 | c.-77G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
| pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
| ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
| Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.41 | cycloserine | |
| clpC1 | 4038933 | p.Ala591Val | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| 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 |
