Run ID: ERR718269
Sample name:
Date: 2025-04-25T03:20:08.423995
Number of reads: 3348835
Percentage reads mapped: 99.65
Median coverage: 62.0
Strain: lineage4.4.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 1.0 |
lineage4.4.2 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Tyr | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Gly406Ala | Assoc w R | |
pyrazinamide | ||||
streptomycin | gid | c.115delC | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | p.Trp69* | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761139 | p.His445Tyr | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
embB | 4247730 | p.Gly406Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4327267 | p.Trp69* | stop_gained | 1.0 | ethionamide | Assoc w R | |
gid | 4408087 | c.115delC | frameshift_variant | 1.0 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7346 | c.45C>T | synonymous_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575582 | c.235C>T | synonymous_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
capreomycin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
folC | 2746540 | c.1059G>T | synonymous_variant | 1.0 | para-aminosalicylic_acid | Uncertain significance |
folC | 2747047 | c.552C>G | synonymous_variant | 1.0 | para-aminosalicylic_acid | Uncertain significance |
Rv2477c | 2783026 | p.Asp339Glu | missense_variant | 1.0 | amikacin | Uncertain significance |
ethambutol | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
Rv2752c | 3066099 | p.Met31Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
isoniazid | Not assoc w R - Interim | |||||
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | Uncertain significance |
Rv3083 | 3448727 | p.Leu75Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3641167 | p.Ile209Val | missense_variant | 0.46 | clofazimine | Uncertain significance |
delamanid | Uncertain significance | |||||
pretomanid | Uncertain significance | |||||
embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243991 | c.759T>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
embA | 4246508 | c.3276G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4268928 | c.906C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269375 | c.459G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethR | 4327617 | p.Asp23Glu | missense_variant | 0.41 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | amikacin | Not assoc w R |
capreomycin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
capreomycin | Uncertain significance | |||||
kanamycin | Uncertain significance |