Run ID: SRR21747063
Sample name:
Date: 2024-10-05T11:48:49.968781
Number of reads: 1548062
Percentage reads mapped: 99.71
Median coverage: 85.0
Strain: lineage2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.1 | East-Asian (non-Beijing) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Leu452Pro | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-16C>G | Uncertain significance | Mutation from literature |
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | mmpR5 | c.181dupG | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.181dupG | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761161 | p.Leu452Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
mmpR5 | 779168 | c.181dupG | frameshift_variant | 0.45 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
embA | 4243217 | c.-16C>G | upstream_gene_variant | 0.62 | ethambutol | Uncertain significance | Mutation from literature |
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 | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 760425 | p.Glu207Lys | missense_variant | 0.24 | rifampicin | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765121 | c.1752G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 778706 | p.Val67Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
mmpR5 | 779062 | p.Gly25Ser | missense_variant | 0.54 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
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 | |||||
fbiC | 1304443 | p.Ala505Thr | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169102 | p.Pro504Leu | missense_variant | 1.0 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2289955 | c.-714C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
Rv2477c | 2783790 | p.Val85Ile | missense_variant | 1.0 | kanamycin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Not assoc w R | |||||
amikacin | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625316 | p.Val433Ala | missense_variant | 0.35 | rifampicin | |
bedaquiline | ||||||
alr | 3841332 | p.Gln30Arg | missense_variant | 1.0 | cycloserine | |
rpoA | 3878702 | c.-195T>G | upstream_gene_variant | 1.0 | rifampicin | |
clpC1 | 4040841 | c.-138delG | upstream_gene_variant | 1.0 | pyrazinamide | |
embC | 4240418 | p.Gly186Cys | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243891 | p.Gly220Glu | missense_variant | 0.99 | ethambutol | Uncertain significance |
embA | 4246088 | c.2856A>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4248953 | p.Asp814Asn | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267647 | p.Asp397Gly | 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 | 4338649 | c.-128C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |