Run ID: ERR067738
Sample name:
Date: 2024-04-13T23:24:49.466761
Number of reads: 4398662
Percentage reads mapped: 99.58
Median coverage: 75.0
Strain: lineage2.2.1;lineage4.3.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.27 |
lineage2 | East-Asian | RD105 | 0.69 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.71 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.74 |
lineage4 | Euro-American | None | 0.3 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.26 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asp | Assoc w R | |
p.Ser450Leu | Assoc w R | |||
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embA | c.-16C>T | Uncertain significance | Mutation from literature |
embB | p.Gly406Cys | Assoc w R | ||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
rrs | n.514A>C | Assoc w R | ||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-10G>A | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | folC | p.Ser150Gly | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 0.25 | rifampicin | Assoc w R | |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.69 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.71 | streptomycin | Assoc w R | |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.26 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.3 | isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R | Alias fabG1_c.-15C>T | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 0.65 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
folC | 2747151 | p.Ser150Gly | missense_variant | 0.73 | para-aminosalicylic_acid | Mutation from literature | |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.72 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247729 | p.Gly406Cys | missense_variant | 0.3 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 698 | p.Arg233Gln | missense_variant | 0.17 | isoniazid | Uncertain significance |
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 | 8040 | p.Gly247Ser | missense_variant | 0.29 | 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 | 0.64 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.68 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.67 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.7 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.72 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.8 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.71 | rifampicin | Uncertain significance |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.29 | rifampicin | Not assoc w R |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.71 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.69 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.67 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.77 | 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 | 0.78 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
fbiC | 1303095 | c.165G>A | synonymous_variant | 0.42 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
fbiC | 1304962 | p.Trp678Gly | missense_variant | 0.3 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
sigE | 1364706 | c.294G>A | synonymous_variant | 0.73 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.61 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.74 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.27 | 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 | 0.74 | isoniazid | Not assoc w R |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.31 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.73 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.27 | isoniazid | |
folC | 2746340 | p.Ala420Val | missense_variant | 0.3 | para-aminosalicylic_acid | |
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 0.24 | para-aminosalicylic_acid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.29 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.72 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.81 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3877981 | p.Tyr176Cys | missense_variant | 0.14 | rifampicin | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.35 | pyrazinamide | Not assoc w R |
clpC1 | 4038968 | c.1737G>A | synonymous_variant | 0.25 | pyrazinamide | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.68 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.73 | ethambutol | Not assoc w R |
ethA | 4326761 | p.Val238Gly | missense_variant | 0.71 | ethionamide | 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 | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.7 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.82 | streptomycin | Not assoc w R |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.29 | streptomycin | Not assoc w R |