Run ID: ERR2747605
Sample name:
Date: 2024-10-05T07:09:52.211981
Number of reads: 650157
Percentage reads mapped: 80.54
Median coverage: 8.0
Strain: La1.8.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1.8 | M.bovis | None | 1.0 |
| La1.8.1 | M.bovis | None | 1.0 |
| La1 | M.bovis | None | 0.3 |
| 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 |
|---|---|---|---|---|---|---|
| dnaA | 467 | p.His156Arg | missense_variant | 1.0 | isoniazid | Not assoc w R |
| 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 | |||||
| Rv0010c | 13197 | p.Thr121Ser | missense_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13228 | c.330delG | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rplC | 801454 | p.Glu216Gln | missense_variant | 1.0 | linezolid | |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| Rv1129c | 1254582 | c.-48A>G | upstream_gene_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| 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 |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| bacA | 2063157 | c.1572C>G | synonymous_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| PPE35 | 2168814 | c.1798dupA | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv2477c | 2782927 | c.1116A>G | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| levofloxacin | Not assoc w R - Interim | |||||
| moxifloxacin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| amikacin | Not assoc w R - Interim | |||||
| Rv2681 | 2997325 | p.Ala196Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
| Rv2752c | 3066555 | c.-364C>T | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| embC | 4242970 | c.3108C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4267858 | p.Ile327Val | missense_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
