Run ID: ERR552160
Sample name:
Date: 2024-10-03T22:14:20.013199
Number of reads: 1149753
Percentage reads mapped: 99.67
Median coverage: 56.0
Strain: lineage4.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
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 |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 4966 | c.-274C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6507 | p.Ala423Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9656 | c.2355C>G | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
ccsA | 620314 | c.424C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
capreomycin | ||||||
amikacin | Not assoc w R - Interim | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765187 | c.1818C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 766012 | c.2643C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 778816 | c.85_89delCGCAC | frameshift_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781421 | c.-139C>A | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.98 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
ndh | 2102702 | p.Ser114Ile | missense_variant | 1.0 | isoniazid | Uncertain significance |
delamanid | ||||||
ethionamide | ||||||
katG | 2156007 | c.105C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
eis | 2714308 | p.Pro342Leu | missense_variant | 1.0 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
Rv2681 | 2997736 | c.1009_1011delCCG | conservative_inframe_deletion | 1.0 | capreomycin | Uncertain significance |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrA | 3627293 | c.57G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
alr | 3840871 | p.Ala184Thr | missense_variant | 1.0 | cycloserine | |
rpoA | 3878876 | c.-369A>G | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
clpC1 | 4039382 | c.1323C>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 |
embC | 4242803 | p.Val981Leu | missense_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 |