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 |