Run ID: ERR038741
Sample name:
Date: 2024-10-05T00:16:53.261715
Number of reads: 10835450
Percentage reads mapped: 99.41
Median coverage: 182.0
Strain: lineage4.2.2.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 1.0 |
lineage4.2 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.2.2.2 | Euro-American (Ural) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asp | Assoc w R | |
isoniazid | ahpC | c.-81C>T | Uncertain significance | Mutation from literature |
ethambutol | embA | c.-16C>T | Uncertain significance | Mutation from literature |
embB | p.Asp354Ala | Assoc w R | ||
pyrazinamide | pncA | c.459_462dupCAGG | Assoc w R | |
streptomycin | ||||
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 | 761139 | p.His445Asp | missense_variant | 0.99 | rifampicin | Assoc w R | |
pncA | 2288779 | c.459_462dupCAGG | frameshift_variant | 0.99 | pyrazinamide | Assoc w R | |
ahpC | 2726112 | c.-81C>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.99 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 305 | p.Pro102Leu | missense_variant | 0.99 | isoniazid | Uncertain significance |
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 | 8688 | p.Ala463Ser | 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 | |||||
mshA | 576077 | c.730C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R - Interim | |||||
Rv0565c | 657425 | p.Gly16Ser | missense_variant | 0.99 | ethionamide | Uncertain significance |
rpoC | 764613 | p.Gln415Arg | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 766163 | p.Glu932Lys | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 | 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 |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.99 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474900 | n.1243G>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rpsA | 1834013 | p.Val158Leu | missense_variant | 1.0 | pyrazinamide | |
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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 0.99 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 1.0 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
katG | 2154224 | p.Gly630Arg | missense_variant | 1.0 | isoniazid | |
PPE35 | 2169044 | c.1569G>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
Rv1979c | 2221919 | p.Val416Met | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
eis | 2714929 | p.Thr135Ser | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
eis | 2715270 | c.63G>C | synonymous_variant | 1.0 | kanamycin | |
amikacin | ||||||
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
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 | ||||||
gid | 4408072 | p.Leu44Arg | missense_variant | 0.99 | streptomycin | Uncertain significance |