Run ID: ERR502504
Sample name:
Date: 2024-10-04T16:33:55.285645
Number of reads: 3784761
Percentage reads mapped: 99.37
Median coverage: 81.0
Strain: lineage4.1.3;lineage6.2.1
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1.3 | Euro-American | None | 0.58 |
lineage6.2 | West-Africa 2 | RD702 | 0.39 |
lineage4.1 | Euro-American | None | 0.61 |
lineage4 | Euro-American | None | 0.58 |
lineage6.2.1 | West-Africa 2 | RD702 | 0.47 |
lineage6 | West-Africa 2 | RD702 | 0.43 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | inhA | c.-154G>A | Assoc w R | Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | p.Leu79Ser | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-154G>A | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.49 | ethionamide | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
isoniazid | Assoc w R | Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.55 | isoniazid | Assoc w R | High-level resistance |
gid | 4407967 | p.Leu79Ser | missense_variant | 0.57 | streptomycin | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5072 | c.-168G>T | upstream_gene_variant | 0.35 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.47 | levofloxacin | Not assoc w R |
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 | 8493 | p.Leu398Phe | missense_variant | 0.4 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.36 | 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 | 9557 | c.2256G>C | synonymous_variant | 0.66 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.26 | isoniazid | Not assoc w R |
Rv0010c | 13482 | p.Ala26Val | missense_variant | 0.28 | isoniazid | Not assoc w R |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 0.48 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.47 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 656432 | p.Gly347Ser | missense_variant | 0.31 | ethionamide | Uncertain significance |
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.65 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.48 | ethionamide | |
rpoB | 760969 | p.Ser388Leu | missense_variant | 0.5 | rifampicin | Not assoc w R |
rpoB | 761723 | p.Glu639Asp | missense_variant | 0.45 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.37 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.55 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.51 | 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 |
rpsL | 781421 | c.-139C>A | upstream_gene_variant | 0.63 | streptomycin | Uncertain significance |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.4 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1129c | 1254607 | c.-73G>C | upstream_gene_variant | 0.47 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.27 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
fbiC | 1304610 | c.1680C>T | synonymous_variant | 0.58 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
Rv1258c | 1406685 | p.Val219Ala | missense_variant | 0.36 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1416633 | p.Leu239Val | missense_variant | 0.4 | ethambutol | Uncertain significance |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.32 | ethambutol | |
atpE | 1461251 | c.207G>T | synonymous_variant | 0.47 | bedaquiline | Not assoc w R - Interim |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
inhA | 1674434 | p.Val78Ala | missense_variant | 0.41 | isoniazid | Not assoc w R |
ethionamide | Uncertain significance | |||||
tsnR | 1854245 | p.Ala214Ser | missense_variant | 0.36 | linezolid | |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917882 | c.-58G>A | upstream_gene_variant | 0.42 | capreomycin | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.44 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063121 | c.1608A>T | synonymous_variant | 0.41 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.4 | isoniazid | Not assoc w R |
katG | 2155503 | c.609C>T | synonymous_variant | 0.41 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.46 | pyrazinamide | Not assoc w R |
PPE35 | 2169269 | c.1340_1344delGCCAAinsT | frameshift_variant&missense_variant | 0.37 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.57 | bedaquiline | Not assoc w R - Interim |
clofazimine | 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 | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.5 | isoniazid | |
Rv2477c | 2783007 | p.Arg346Cys | missense_variant | 0.43 | kanamycin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
ald | 3086728 | c.-92C>T | upstream_gene_variant | 0.33 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087084 | c.266delA | frameshift_variant | 0.43 | cycloserine | |
Rv3236c | 3612800 | p.Val106Ala | missense_variant | 0.43 | pyrazinamide | Uncertain significance |
lpqB | 3623291 | c.1620C>A | synonymous_variant | 0.63 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
lpqB | 3624350 | c.561G>T | synonymous_variant | 0.54 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.38 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
lpqB | 3624660 | p.Ala84Gly | missense_variant | 0.49 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
lpqB | 3625459 | c.-549C>T | upstream_gene_variant | 0.43 | rifampicin | |
bedaquiline | ||||||
alr | 3840559 | p.Arg288Ser | missense_variant | 0.32 | cycloserine | |
alr | 3840618 | p.Asp268Gly | missense_variant | 0.34 | cycloserine | |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.53 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
glpK | 4139183 | c.572dupG | frameshift_variant | 0.42 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 0.49 | ethambutol | Not assoc w R |
embC | 4241843 | p.Leu661Ile | missense_variant | 0.39 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.5 | ethambutol | Not assoc w R |
embA | 4243541 | c.309C>T | synonymous_variant | 0.37 | ethambutol | Not assoc w R - Interim |
embA | 4244220 | c.988C>T | synonymous_variant | 0.59 | ethambutol | Not assoc w R |
embA | 4244379 | p.Pro383Ser | missense_variant | 0.44 | ethambutol | Not assoc w R |
embB | 4246864 | c.351C>T | synonymous_variant | 0.44 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.46 | ethambutol | Not assoc w R |
ubiA | 4269351 | c.483C>T | synonymous_variant | 0.39 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.41 | ethambutol | Not assoc w R |
ubiA | 4269522 | c.312C>T | synonymous_variant | 0.34 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.43 | ethambutol | Not assoc w R |
ethA | 4326465 | p.Ile337Val | missense_variant | 0.39 | 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 | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.44 | streptomycin | Not assoc w R |