Run ID: ERR11775060
Sample name:
Date: 2024-05-22T16:00:18.043199
Number of reads: 6055283
Percentage reads mapped: 99.81
Median coverage: 192.0
Strain: lineage4.9.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.9.1 | Euro-American (H37Rv-like) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | 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 |
ahpC | c.-52C>T | Uncertain significance | Mutation from literature | |
ethambutol | ||||
pyrazinamide | pncA | p.Asp8Tyr | Assoc w R - Interim | |
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 | 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 |
pncA | 2289220 | p.Asp8Tyr | missense_variant | 1.0 | pyrazinamide | Assoc w R - Interim | |
ahpC | 2726141 | c.-52C>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
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 | 8978 | c.1677C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
mshA | 575252 | c.-96C>A | upstream_gene_variant | 1.0 | ethionamide | |
isoniazid | 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 |
rpsL | 781609 | p.Ser17Asn | missense_variant | 0.99 | streptomycin | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 | |||||
pncA | 2289138 | p.Leu35Arg | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
fbiD | 3339385 | p.Asp90Asn | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
embC | 4239257 | c.-606G>C | upstream_gene_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 |