Run ID: ERR7910853
Sample name:
Date: 2024-10-03T20:19:20.809705
Number of reads: 1771254
Percentage reads mapped: 99.65
Median coverage: 51.0
Strain: lineage4.3.4.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4.3.4.1 | Euro-American (LAM) | RD174 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 1.0 |
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.Asp435Gly | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | c.371dupT | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761108 | p.Met434Ile | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpoB | 761110 | p.Asp435Gly | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
gid | 4407831 | c.371dupT | frameshift_variant | 1.0 | streptomycin | 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 | |||||
hadA | 731927 | c.-3G>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
rpoB | 761167 | p.Pro454Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
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 | 0.98 | streptomycin | Not assoc w R |
sigE | 1364434 | p.Arg8Trp | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1853603 | c.-3C>T | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
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 |
katG | 2155787 | p.Ala109Thr | missense_variant | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726323 | p.Pro44Arg | missense_variant | 1.0 | isoniazid | Uncertain significance |
thyX | 3067657 | p.Arg97Trp | missense_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv3236c | 3612896 | p.Gly74Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4248320 | p.Gly603Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
ubiA | 4269721 | p.Ala38Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
ethA | 4327311 | p.Ser55Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
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 | 4338761 | c.-240C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |