TB-Profiler result

Run: ddeb943e-0aa8-4c0b-abe1-c4d639d4c3b1
Summary

Run ID: ddeb943e-0aa8-4c0b-abe1-c4d639d4c3b1

Sample name:

Date: 18-03-2024 09:25:46

Number of reads: 1443066

Percentage reads mapped: 94.43

Median coverage: 16

Strain: lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
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: This table reports drug-resistance associated mutations found in known resistance genes
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
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
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