Run ID: ERR2516401
Sample name:
Date: 2024-10-04T19:00:35.867522
Number of reads: 2321596
Percentage reads mapped: 99.65
Median coverage: 46.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.7 | Euro-American (mainly T) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Trp149* | Assoc w R | High-level resistance |
ahpC | c.-54C>T | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Tyr319Ser | Assoc w R | |
pyrazinamide | pncA | c.151dupC | Assoc w R | |
streptomycin | ||||
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 |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155665 | p.Trp149* | stop_gained | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289090 | c.151dupC | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
ahpC | 2726139 | c.-54C>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247469 | p.Tyr319Ser | missense_variant | 1.0 | ethambutol | 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 | |||||
mshA | 576401 | c.1056delC | frameshift_variant | 0.33 | isoniazid | Uncertain significance |
ethionamide | 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 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474294 | n.637C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
ndh | 2102024 | c.1018dupG | frameshift_variant | 0.73 | isoniazid | Uncertain significance |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249732 | c.3219C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326113 | p.Pro454Leu | missense_variant | 0.65 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
gid | 4407929 | p.Glu92Gln | missense_variant | 1.0 | streptomycin | Uncertain significance |