Run ID: ERR1034843
Sample name:
Date: 2024-04-16T06:46:01.957331
Number of reads: 7209865
Percentage reads mapped: 99.61
Median coverage: 152.0
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.Asp435Tyr | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | pncA | p.Leu159Pro | 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 | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288766 | p.Leu159Pro | missense_variant | 0.87 | pyrazinamide | Assoc w R - Interim |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1126 | c.1126C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
gyrA | 7270 | c.-32C>T | upstream_gene_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 | |||||
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 |
sigE | 1365175 | p.Pro255Ser | missense_variant | 0.99 | pyrazinamide | |
Rv1258c | 1407604 | c.-264C>T | upstream_gene_variant | 0.99 | streptomycin | |
isoniazid | ||||||
pyrazinamide | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
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 | 2102120 | p.Asp308Gly | missense_variant | 0.84 | ethionamide | |
delamanid | ||||||
isoniazid | Uncertain significance | |||||
PPE35 | 2170675 | c.-63G>C | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3087528 | p.Gly237Trp | missense_variant | 1.0 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249562 | p.Asp1017Asn | missense_variant | 0.92 | ethambutol | |
embB | 4249732 | c.3219C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
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 | 4407799 | p.Val135Gly | missense_variant | 1.0 | streptomycin | Uncertain significance |