Run ID: SRR26399250
Sample name:
Date: 2024-10-05T10:48:58.466948
Number of reads: 1619434
Percentage reads mapped: 99.11
Median coverage: 44.0
Strain: lineage1.1.1;lineage2.2.1;lineage4.1.2.1
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.33 |
lineage4.1.2 | Euro-American | None | 0.58 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.62 |
lineage1.1 | Indo-Oceanic | RD239 | 0.06 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.29 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.33 |
lineage4 | Euro-American | None | 0.62 |
lineage1.1.1 | Indo-Oceanic | RD239 | 0.06 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | c.102delG | 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 |
---|---|---|---|---|---|---|---|
gid | 4408100 | c.102delG | frameshift_variant | 0.66 | streptomycin | 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 | |||||
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.23 | isoniazid | Not assoc w R |
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.28 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.44 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.78 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
mshA | 576602 | p.Arg419Trp | missense_variant | 0.62 | isoniazid | |
ethionamide | ||||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.4 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.29 | ethionamide | Uncertain significance |
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.71 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.17 | ethionamide | |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.68 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.65 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.18 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.19 | rifampicin | Not assoc w R |
rpoC | 764061 | p.Pro231Arg | missense_variant | 0.51 | rifampicin | |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.43 | 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 | 0.35 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.38 | 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 | 0.62 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.29 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.2 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
inhA | 1673261 | c.-941C>T | upstream_gene_variant | 0.68 | isoniazid | |
ethionamide | ||||||
inhA | 1673406 | c.-796C>G | upstream_gene_variant | 0.5 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.31 | 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 |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.15 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063106 | c.1623G>A | synonymous_variant | 0.17 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.48 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.56 | pyrazinamide | Not assoc w R |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.13 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.56 | isoniazid | |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.16 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.97 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.21 | ethionamide | Uncertain significance |
Rv3236c | 3613097 | p.Leu7Pro | missense_variant | 0.54 | pyrazinamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.18 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.23 | pyrazinamide | Not assoc w R - Interim |
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.62 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.17 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.64 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.16 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.21 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.37 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.17 | 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 | 0.44 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.21 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.27 | streptomycin | Not assoc w R |