Run ID: SRR28351224
Sample name:
Date: 2024-05-22T11:24:18.216046
Number of reads: 9065129
Percentage reads mapped: 99.75
Median coverage: 284.0
Strain: lineage2.2.1;lineage4.3.4.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.82 |
lineage2 | East-Asian | RD105 | 0.12 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.14 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.13 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 0.86 |
lineage4 | Euro-American | None | 0.87 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.84 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Ile491Thr | Uncertain significance | Mutation from literature | |
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 | eis | c.-37G>T | Assoc w R | |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.19 | rifampicin | Assoc w R | |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.14 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.17 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.15 | isoniazid | Assoc w R | High-level resistance |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.19 | kanamycin | 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 | 13636 | c.-78A>G | upstream_gene_variant | 0.15 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.2 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.16 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 763783 | c.414G>A | synonymous_variant | 0.83 | rifampicin | Not assoc w R - Interim |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.84 | rifampicin | Not assoc w R |
rpoC | 765325 | c.1956C>T | synonymous_variant | 0.83 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.17 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.15 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
sigE | 1364434 | p.Arg8Trp | missense_variant | 0.87 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.19 | 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 | 0.99 | capreomycin | Not assoc w R |
PPE35 | 2168147 | c.2466A>G | synonymous_variant | 0.87 | pyrazinamide | Not assoc w R - Interim |
PPE35 | 2169016 | p.Thr533Ala | missense_variant | 0.17 | pyrazinamide | Uncertain significance |
Rv1979c | 2223123 | c.42G>A | synonymous_variant | 0.76 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
folC | 2746540 | c.1059G>A | synonymous_variant | 0.84 | para-aminosalicylic_acid | |
folC | 2746747 | c.852G>C | synonymous_variant | 0.17 | para-aminosalicylic_acid | |
Rv2681 | 2996821 | p.Gly28Ala | missense_variant | 0.85 | capreomycin | Uncertain significance |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.84 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.81 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840710 | c.711A>G | synonymous_variant | 0.92 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.86 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4327247 | p.Ala76Asp | missense_variant | 0.16 | ethionamide | Uncertain significance |
whiB6 | 4338550 | c.-29A>T | upstream_gene_variant | 0.85 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
whiB6 | 4338735 | c.-214C>G | upstream_gene_variant | 0.91 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407927 | p.Glu92Asp | missense_variant | 0.16 | streptomycin | Not assoc w R |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.87 | streptomycin | Not assoc w R |