Run ID: ERR4020182
Sample name:
Date: 2024-04-15T13:53:29.873290
Number of reads: 3610510
Percentage reads mapped: 99.73
Median coverage: 106.0
Strain: lineage4.3.4.2.1;lineage4.4.1.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.2 |
lineage4.4.1 | Euro-American (S-type) | None | 0.79 |
lineage4 | Euro-American | None | 1.0 |
lineage4.4.1.1 | Euro-American | None | 0.77 |
lineage4.3.4.2.1 | Euro-American (LAM) | RD174 | 0.19 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.2 |
lineage4.3.4.2 | Euro-American (LAM) | RD174 | 0.21 |
lineage4.4 | Euro-American | None | 0.78 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Met434Ile | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
p.Ser450Trp | Assoc w R | |||
p.Ile491Phe | Assoc w R | |||
rpoC | p.Ile491Thr | Uncertain significance | Mutation from literature | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
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 | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761108 | p.Met434Ile | missense_variant | 0.78 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpoB | 761155 | p.Ser450Trp | missense_variant | 0.24 | rifampicin | Assoc w R | |
rpoB | 761277 | p.Ile491Phe | missense_variant | 0.72 | rifampicin | Assoc w R | |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.16 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.84 | 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 | 0.84 | pyrazinamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 0.26 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 0.83 | 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 | |||||
rpoB | 761406 | p.Val534Met | missense_variant | 0.88 | rifampicin | Uncertain significance |
rpoB | 761558 | c.1752C>G | synonymous_variant | 0.22 | rifampicin | Not assoc w R - Interim |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 777416 | c.1065G>T | synonymous_variant | 0.79 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1258c | 1406353 | p.Pro330Thr | missense_variant | 0.28 | streptomycin | |
isoniazid | ||||||
pyrazinamide | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.1 | ethionamide | |
isoniazid | ||||||
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 | 0.81 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
PPE35 | 2168479 | p.Thr712Pro | missense_variant | 0.75 | pyrazinamide | Not assoc w R |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 0.76 | pyrazinamide | 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 | |||||
kasA | 2518496 | c.382C>T | synonymous_variant | 0.8 | isoniazid | |
Rv2752c | 3065023 | p.Pro390Leu | missense_variant | 0.84 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.2 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448522 | p.Val7Phe | missense_variant | 0.78 | ethionamide | Uncertain significance |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 0.81 | ethionamide | Not assoc w R - Interim |
whiB7 | 3568779 | c.-100T>C | upstream_gene_variant | 0.8 | streptomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.2 | pyrazinamide | Not assoc w R |
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 0.73 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840719 | c.702A>G | synonymous_variant | 0.18 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.28 | pyrazinamide | Not assoc w R |
glpK | 4138401 | c.1354delG | frameshift_variant | 0.81 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.82 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247429 | c.916_918delATGinsGA | frameshift_variant&missense_variant | 0.21 | ethambutol | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 0.27 | streptomycin | Not assoc w R |