Run ID: 36a91f8f-1b0d-4c4c-bc9d-877644e37110
Sample name:
Date: 24-01-2023 11:17:34
Number of reads: 67252
Percentage reads mapped: 96.26
Median coverage: 0
Strain: lineage2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.98 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Gln10Lys | Uncertain significance | |
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | |
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | eis | c.-14C>T | Assoc w R | |
kanamycin | eis | c.-14C>T | Assoc w R | |
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.97 | ofloxacin | Uncertain significance | |
moxifloxacin | Assoc w R | ||||||
levofloxacin | Assoc w R | ||||||
fluoroquinolones | Uncertain significance | ||||||
ciprofloxacin | Uncertain significance | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.97 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid | Assoc w R | |
pncA | 2289214 | p.Gln10Lys | missense_variant | 0.99 | pyrazinamide | Uncertain significance | |
eis | 2715346 | c.-14C>T | upstream_gene_variant | 0.85 | kanamycin | Assoc w R | |
amikacin | Assoc w R | ||||||
embB | 4247429 | p.Met306Val | missense_variant | 0.98 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.94 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.95 | rifampicin | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.93 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.81 | pyrazinamide | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.98 | capreomycin | |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.88 | isoniazid | Uncertain significance |
ribD | 2987091 | p.Val85Met | missense_variant | 0.94 | para-aminosalicylic_acid | |
ald | 3087246 | p.Gln143* | stop_gained | 0.83 | cycloserine | |
ethR | 4327941 | p.Ser131Arg | missense_variant | 0.99 | ethionamide | Uncertain significance |
gid | 4407588 | c.615A>G | synonymous_variant | 0.98 | streptomycin | |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.96 | streptomycin | Uncertain significance |