Run ID: ERR2653126
Sample name:
Date: 2024-10-04T14:37:53.414467
Number of reads: 8910472
Percentage reads mapped: 97.6
Median coverage: 259.0
Strain: lineage4.4.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1 | Euro-American (S-type) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4.1.1 | Euro-American | None | 1.0 |
lineage4.4 | 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.Asp354Ala | Assoc w R | |
pyrazinamide | pncA | c.193_200dupTCCTCGTC | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.110delA | 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 | 0.98 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289041 | c.193_200dupTCCTCGTC | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4327363 | c.110delA | frameshift_variant | 1.0 | ethionamide | 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 | |||||
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 | |||||
rpoC | 765804 | p.Thr812Ile | missense_variant | 0.99 | rifampicin | 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 | ||||||
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 |
ndh | 2102990 | p.Val18Ala | missense_variant | 1.0 | isoniazid | Not assoc w R |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2170646 | c.-34T>C | upstream_gene_variant | 0.99 | pyrazinamide | |
Rv1979c | 2222760 | p.Ser135Arg | missense_variant | 0.99 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2477c | 2784264 | c.-223delC | upstream_gene_variant | 0.98 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
whiB7 | 3568665 | c.15A>G | synonymous_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3641010 | c.468C>T | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
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 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338783 | c.-262C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407973 | p.Val77Ala | missense_variant | 1.0 | streptomycin | Uncertain significance |