Run ID: ERR2503450
Sample name:
Date: 2024-10-04T12:44:01.612912
Number of reads: 445988
Percentage reads mapped: 99.59
Median coverage: 22.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | c.351delG | 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 |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
gid | 4407851 | c.351delG | 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 | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
Rv0565c | 656837 | p.Ser212Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
nusG | 734735 | p.Ala161Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
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 | 1.0 | streptomycin | Not assoc w R |
Rv1258c | 1406101 | p.Pro414Ser | missense_variant | 1.0 | streptomycin | Uncertain significance |
pyrazinamide | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R | |||||
embR | 1416528 | p.Val274Phe | missense_variant | 1.0 | ethambutol | |
atpE | 1460820 | c.-225G>A | upstream_gene_variant | 1.0 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1853597 | c.-9G>C | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
PPE35 | 2170568 | p.Ile15Met | 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 | |||||
Rv3083 | 3448675 | p.Asp58His | missense_variant | 1.0 | ethionamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
alr | 3841546 | c.-126C>A | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841568 | c.-148G>A | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841570 | c.-151delA | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841574 | c.-154T>G | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841578 | c.-158G>T | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841582 | c.-162A>G | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841584 | c.-164C>A | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841589 | c.-170delG | upstream_gene_variant | 1.0 | cycloserine | |
alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 1.0 | cycloserine | |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4039745 | c.960C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4327205 | p.Ala90Val | missense_variant | 1.0 | ethionamide | |
whiB6 | 4338594 | c.-73T>A | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
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 | 4408398 | c.-196C>G | upstream_gene_variant | 1.0 | streptomycin |