Run ID: 7edf5604-d9c0-4c7a-9513-e70ccce99f66
Sample name:
Date: 18-03-2024 11:22:45
Number of reads: 1443066
Percentage reads mapped: 94.43
Median coverage: 16
Strain: lineage6.3.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage6 | West-Africa 2 | RD702 | 0.99 |
lineage6.3 | West-Africa 2 | RD702 | 0.99 |
lineage6.3.1 | West-Africa 2 | RD702 | 0.96 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
moxifloxacin | ||||
levofloxacin | ||||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9725 | p.Glu808Asp | missense_variant | 0.13 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
fgd1 | 490621 | c.-162C>G | upstream_gene_variant | 0.13 | delamanid | |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 0.93 | delamanid | Uncertain significance |
fgd1 | 491740 | p.Phe320Leu | missense_variant | 0.12 | delamanid | |
ccsA | 620710 | p.Val274Leu | missense_variant | 0.11 | capreomycin | |
amikacin | ||||||
rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 761591 | p.Asp595Glu | missense_variant | 0.2 | rifampicin | Uncertain significance |
rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoB | 762285 | p.Arg827Cys | missense_variant | 0.11 | rifampicin | Uncertain significance |
rpoC | 762950 | c.-420G>A | upstream_gene_variant | 0.2 | rifampicin | |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 763526 | p.Gly53Arg | missense_variant | 0.15 | rifampicin | |
rpoC | 765284 | p.Gln639Lys | missense_variant | 0.14 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776041 | p.Ala814Ser | missense_variant | 0.1 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 776054 | c.2427G>T | synonymous_variant | 0.11 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 776702 | c.1779C>T | synonymous_variant | 0.11 | clofazimine | |
bedaquiline | ||||||
mmpL5 | 776726 | c.1755C>T | synonymous_variant | 0.15 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | delamanid | Uncertain significance |
fbiC | 1305349 | c.2419C>T | synonymous_variant | 0.14 | delamanid | |
Rv1258c | 1406217 | p.Gly375Val | missense_variant | 0.13 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
Rv1258c | 1406363 | c.978A>G | synonymous_variant | 0.83 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
embR | 1416232 | p.Cys372Gly | missense_variant | 0.12 | ethambutol | |
embR | 1416945 | p.Ser135Gly | missense_variant | 0.18 | ethambutol | |
atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rpsA | 1833723 | p.Gly61Val | missense_variant | 0.17 | pyrazinamide | |
rpsA | 1834616 | p.Ser359Pro | missense_variant | 0.13 | pyrazinamide | |
ndh | 2102422 | c.621C>G | synonymous_variant | 0.12 | ethionamide | |
isoniazid | ||||||
ndh | 2102694 | p.Val117Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
katG | 2153908 | p.Asp735Gly | missense_variant | 0.12 | isoniazid | |
katG | 2154514 | p.Pro533Arg | missense_variant | 0.11 | isoniazid | |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
PPE35 | 2168342 | c.2271T>G | synonymous_variant | 0.12 | pyrazinamide | |
PPE35 | 2169602 | c.1011C>A | synonymous_variant | 0.18 | pyrazinamide | |
PPE35 | 2169623 | c.990T>C | synonymous_variant | 0.17 | pyrazinamide | |
PPE35 | 2170466 | c.147A>G | synonymous_variant | 0.18 | pyrazinamide | |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2222804 | p.Ala121Ser | missense_variant | 0.12 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
pncA | 2289189 | p.Ser18Leu | missense_variant | 0.15 | pyrazinamide | |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
kasA | 2518183 | c.69G>T | synonymous_variant | 0.14 | isoniazid | |
eis | 2715146 | p.Leu63Met | missense_variant | 0.1 | kanamycin | |
amikacin | ||||||
pepQ | 2859567 | c.852C>A | synonymous_variant | 0.14 | clofazimine | |
bedaquiline | ||||||
pepQ | 2859571 | p.Asp283Gly | missense_variant | 0.14 | clofazimine | |
bedaquiline | ||||||
pepQ | 2859576 | p.Ile281Met | missense_variant | 0.15 | clofazimine | |
bedaquiline | ||||||
pepQ | 2860263 | c.156C>T | synonymous_variant | 0.15 | clofazimine | |
bedaquiline | ||||||
ribD | 2986651 | c.-188G>T | upstream_gene_variant | 0.11 | para-aminosalicylic_acid | |
ribD | 2986792 | c.-47C>A | upstream_gene_variant | 0.11 | para-aminosalicylic_acid | |
ribD | 2987093 | c.255G>T | synonymous_variant | 0.1 | para-aminosalicylic_acid | |
Rv2752c | 3065379 | c.813C>A | synonymous_variant | 0.15 | rifampicin | |
isoniazid | ||||||
Rv2752c | 3066128 | p.Gly22Ser | missense_variant | 0.1 | rifampicin | |
isoniazid | ||||||
thyA | 3074238 | c.234C>G | synonymous_variant | 0.12 | para-aminosalicylic_acid | |
ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086958 | p.Asp47Tyr | missense_variant | 1.0 | cycloserine | |
fbiD | 3339270 | c.153G>A | synonymous_variant | 0.12 | delamanid | |
Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 1.0 | ethionamide | |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
Rv3236c | 3612173 | p.Arg315Gln | missense_variant | 0.15 | pyrazinamide | Uncertain significance |
Rv3236c | 3613307 | c.-191G>T | upstream_gene_variant | 0.18 | pyrazinamide | Uncertain significance |
fbiA | 3640402 | c.-141C>T | upstream_gene_variant | 0.11 | delamanid | |
fbiB | 3641430 | c.-105T>G | upstream_gene_variant | 0.1 | delamanid | |
rpoA | 3877696 | p.Thr271Ile | missense_variant | 0.87 | rifampicin | Uncertain significance |
clpC1 | 4040489 | c.216G>A | synonymous_variant | 1.0 | pyrazinamide | |
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4241188 | c.1326C>A | synonymous_variant | 0.1 | ethambutol | |
embC | 4241587 | c.1725C>A | synonymous_variant | 0.12 | ethambutol | |
embC | 4241797 | p.Asn645Lys | missense_variant | 0.14 | ethambutol | |
embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4245340 | p.Gly703Asp | missense_variant | 0.15 | ethambutol | |
embA | 4245507 | p.Gly759* | stop_gained | 0.15 | ethambutol | |
embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4247884 | c.1371C>T | synonymous_variant | 0.13 | ethambutol | |
embB | 4248735 | p.Arg741Leu | missense_variant | 0.17 | ethambutol | |
aftB | 4268477 | c.360C>T | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4269522 | c.-686C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
ubiA | 4269859 | c.-26A>C | upstream_gene_variant | 0.14 | ethambutol | |
ubiA | 4270031 | c.-198G>A | upstream_gene_variant | 0.18 | ethambutol | |
ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
ethA | 4327346 | p.Gly43Val | missense_variant | 0.12 | ethionamide | Uncertain significance |
whiB6 | 4338176 | p.Ala116Thr | missense_variant | 0.19 | streptomycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin |