Run ID: ERR8975639
Sample name:
Date: 2024-10-03T18:22:40.273079
Number of reads: 3126410
Percentage reads mapped: 99.72
Median coverage: 108.0
Strain: lineage4.4.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.4.1 | Euro-American (S-type) | None | 0.94 |
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.Ile491Phe | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.His51Asp | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | pepQ | c.949_950insA | Assoc w R - Interim | |
c.594dupC | Assoc w R - Interim | |||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | pepQ | c.949_950insA | Assoc w R - Interim | Includes data from one site that only submitted resistant strains, which may have inflated the PPV |
c.594dupC | Assoc w R - Interim | Includes data from one site that only submitted resistant strains, which may have inflated the PPV | ||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761277 | p.Ile491Phe | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289091 | p.His51Asp | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
pepQ | 2859469 | c.949_950insA | frameshift_variant | 0.18 | bedaquiline | Assoc w R - Interim | Includes data from one site that only submitted resistant strains, which may have inflated the PPV |
clofazimine | Assoc w R - Interim | ||||||
pepQ | 2859824 | c.594dupC | frameshift_variant | 0.45 | bedaquiline | Assoc w R - Interim | Includes data from one site that only submitted resistant strains, which may have inflated the PPV |
clofazimine | Assoc w R - Interim | ||||||
embB | 4247431 | p.Met306Ile | 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 | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9138 | p.Gln613Glu | 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 | |||||
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 777416 | c.1065G>T | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | 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 | 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 | |||||
katG | 2156148 | c.-37T>C | upstream_gene_variant | 0.28 | isoniazid | |
PPE35 | 2168479 | p.Thr712Pro | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518496 | c.382C>T | synonymous_variant | 1.0 | isoniazid | |
Rv2752c | 3065023 | p.Pro390Leu | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448522 | p.Val7Phe | missense_variant | 1.0 | ethionamide | Uncertain significance |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
whiB7 | 3568779 | c.-100T>C | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
amikacin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
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 | |||||
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 |