Run ID: SRR28393252
Sample name:
Date: 2024-05-22T16:25:06.271093
Number of reads: 5580003
Percentage reads mapped: 99.59
Median coverage: 144.0
Strain: lineage4.3.3;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 | 0.82 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.15 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.82 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asp | Assoc w R | |
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) |
p.Ile21Thr | Uncertain significance | Mutation from literature | ||
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Asp136Tyr | Uncertain significance | Mutation from literature |
p.His51Arg | Assoc w R | |||
streptomycin | gid | c.180delA | 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 |
p.Ile21Thr | Uncertain significance | Mutation from literature | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761139 | p.His445Asp | missense_variant | 0.9 | rifampicin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.2 | 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) | |||||
inhA | 1674263 | p.Ile21Thr | missense_variant | 0.13 | ethionamide | Uncertain significance | Mutation from literature |
isoniazid | Uncertain significance | Mutation from literature | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.8 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288836 | p.Asp136Tyr | missense_variant | 0.86 | pyrazinamide | Uncertain significance | Mutation from literature |
pncA | 2289090 | p.His51Arg | missense_variant | 0.27 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 0.83 | ethambutol | Assoc w R | |
gid | 4408022 | c.180delA | frameshift_variant | 0.85 | 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 | |||||
rpoC | 764532 | p.Gly388Ala | missense_variant | 0.84 | rifampicin | Uncertain significance |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765590 | p.Arg741Ser | missense_variant | 0.85 | rifampicin | Uncertain significance |
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 | 1364434 | p.Arg8Trp | missense_variant | 0.82 | pyrazinamide | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834378 | c.837T>C | synonymous_variant | 0.84 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834683 | p.Ala381Val | missense_variant | 0.18 | pyrazinamide | 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 |
Rv1979c | 2223123 | c.42G>A | synonymous_variant | 0.81 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.22 | isoniazid | |
Rv2477c | 2784248 | c.-206C>G | upstream_gene_variant | 0.12 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.99 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.8 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
glpK | 4139183 | c.572dupG | frameshift_variant | 0.23 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242182 | p.Ala774Ser | missense_variant | 0.17 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269341 | p.Gly165Ser | missense_variant | 0.19 | ethambutol | Uncertain significance |
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 | 1.0 | streptomycin | Not assoc w R |