Run ID: SRR23861707
Sample name:
Date: 2024-10-04T19:50:40.483787
Number of reads: 2411694
Percentage reads mapped: 99.52
Median coverage: 66.0
Strain: lineage2.2.1;lineage4.2.1
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.16 |
lineage4.2 | Euro-American | None | 0.83 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.12 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.15 |
lineage4 | Euro-American | None | 0.89 |
lineage4.2.1 | Euro-American (TUR) | None | 0.84 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.88 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.95 | isoniazid | Assoc w R | High-level resistance |
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 | |||||
Rv0010c | 13640 | c.-82T>C | upstream_gene_variant | 0.55 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.23 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.19 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.24 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.24 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.17 | 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 | 0.15 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.11 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.83 | linezolid | |
Rv1129c | 1253963 | p.Asp191Gly | missense_variant | 0.88 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.22 | 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 | 0.14 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.12 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
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 | 2063685 | c.1044G>A | synonymous_variant | 0.73 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.93 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.17 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.18 | pyrazinamide | Not assoc w R |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.78 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2477c | 2783731 | c.312C>T | synonymous_variant | 0.95 | kanamycin | Not assoc w R - Interim |
levofloxacin | Not assoc w R - Interim | |||||
moxifloxacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.85 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448456 | c.-48G>A | upstream_gene_variant | 0.76 | ethionamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.15 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4038932 | c.1773G>A | synonymous_variant | 0.82 | pyrazinamide | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.15 | ethambutol | Not assoc w R |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.95 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.2 | ethambutol | Not assoc w R |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.88 | ethionamide | |
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 | 0.13 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.12 | streptomycin | Not assoc w R |