Run ID: ERR2041701
Sample name:
Date: 2024-03-24T15:31:05.223926
Number of reads: 923046
Percentage reads mapped: 98.32
Median coverage: 26.0
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.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | c.395_406delGTATTGCCACCG | Mutation from literature | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.752dupG | Assoc w R | |
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 | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288835 | c.395_406delGTATTGCCACCG | disruptive_inframe_deletion | 1.0 | pyrazinamide | Mutation from literature | |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326721 | c.752dupG | frameshift_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6358 | c.1119C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 574786 | c.-561_*636del | transcript_ablation | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
rpoC | 764916 | p.Leu516Pro | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
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 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471778 | n.-68G>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | Uncertain significance | |||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
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 |
ubiA | 4269323 | p.Pro171Ser | missense_variant | 1.0 | ethambutol | 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 | |||||
gid | 4407980 | p.Pro75Ser | missense_variant | 1.0 | streptomycin | Uncertain significance |