Run ID: SRR29539525
Sample name:
Date: 2024-10-04T01:30:29.425417
Number of reads: 4148988
Percentage reads mapped: 99.61
Median coverage: 119.0
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Leu | Assoc w R | |
p.Asp1024Asn | Uncertain significance | Mutation from literature | ||
pyrazinamide | pncA | c.433delG | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.191dupT | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288808 | c.433delG | frameshift_variant | 0.62 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Leu | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4249583 | p.Asp1024Asn | missense_variant | 0.65 | ethambutol | Uncertain significance | Mutation from literature |
ethA | 4327282 | c.191dupT | frameshift_variant | 1.0 | ethionamide | Assoc w R |
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 | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | 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 | 761407 | p.Val534Ala | missense_variant | 0.55 | rifampicin | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 764703 | p.Lys445Arg | missense_variant | 0.47 | rifampicin | Uncertain significance |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 1.0 | rifampicin | Not assoc w R |
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 | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | 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 | |||||
sigE | 1364706 | c.294G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | 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 | 2169335 | c.1278C>T | synonymous_variant | 0.12 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2289055 | p.Asp63Tyr | missense_variant | 0.22 | pyrazinamide | |
ahpC | 2726354 | c.162G>T | synonymous_variant | 0.14 | isoniazid | |
thyA | 3074495 | c.-24C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612229 | c.888C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
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 | 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 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |