TB-Profiler result

Run: c8ce5037-7956-443a-9359-3c5182aaa8ea
Summary

Run ID: c8ce5037-7956-443a-9359-3c5182aaa8ea

Sample name:

Date: 08-04-2024 09:51:29

Number of reads: 334061

Percentage reads mapped: 99.15

Median coverage: 14

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R
ethambutol
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9605 c.2304C>T synonymous_variant 0.17 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
ccsA 619831 c.-60T>G upstream_gene_variant 0.38 capreomycin
amikacin
rpoB 759620 c.-187A>C upstream_gene_variant 0.21 rifampicin
rpoB 760013 c.207C>T synonymous_variant 0.11 rifampicin
rpoB 761730 p.Gly642Ser missense_variant 0.15 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1303257 c.328delG frameshift_variant 0.17 delamanid
fbiC 1303260 c.330G>T synonymous_variant 0.17 delamanid
Rv1258c 1406497 p.Ala282Ser missense_variant 0.18 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407354 c.-14C>T upstream_gene_variant 0.18 streptomycin
pyrazinamide
isoniazid
rrl 1473556 n.-102T>G upstream_gene_variant 0.15 linezolid
rpsA 1834661 p.Asp374Asn missense_variant 0.18 pyrazinamide
ndh 2101775 p.Ser423Asn missense_variant 0.15 ethionamide
isoniazid
katG 2156150 c.-39G>A upstream_gene_variant 0.1 isoniazid
PPE35 2168192 c.2421T>C synonymous_variant 0.17 pyrazinamide
PPE35 2169504 p.Gly370Asp missense_variant 0.2 pyrazinamide
Rv1979c 2222200 p.Gly322Val missense_variant 0.11 clofazimine
bedaquiline
Rv1979c 2222491 p.Thr225Met missense_variant 0.17 clofazimine
bedaquiline
Rv1979c 2222683 p.Trp161* stop_gained 0.15 clofazimine
bedaquiline
Rv1979c 2222751 c.414G>A synonymous_variant 0.14 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ahpC 2726628 p.Phe146Val missense_variant 1.0 isoniazid
thyA 3073687 p.Ala262Glu missense_variant 0.15 para-aminosalicylic_acid
thyA 3074058 c.414C>T synonymous_variant 0.17 para-aminosalicylic_acid
thyA 3074654 c.-183T>G upstream_gene_variant 0.2 para-aminosalicylic_acid
ald 3086738 c.-81delG upstream_gene_variant 0.13 cycloserine
Rv3083 3449305 p.Leu268Val missense_variant 0.18 ethionamide
fprA 3474145 p.Gly47Trp missense_variant 0.15 capreomycin
amikacin
fprA 3474276 c.272delG frameshift_variant 0.14 capreomycin
amikacin
fprA 3474365 p.Pro120Leu missense_variant 0.17 capreomycin
amikacin
whiB7 3568708 c.-29A>T upstream_gene_variant 0.11 streptomycin
kanamycin
amikacin
ddn 3986966 p.Phe41Leu missense_variant 0.11 delamanid
ddn 3987031 p.Pro63Leu missense_variant 0.12 delamanid
clpC1 4039573 p.Ala378Thr missense_variant 0.12 pyrazinamide
panD 4044047 p.Val79Leu missense_variant 0.15 pyrazinamide
embC 4240881 p.Ala340Val missense_variant 0.14 ethambutol
embC 4241225 p.Pro455Thr missense_variant 0.13 ethambutol
embC 4242704 p.Asp948Tyr missense_variant 0.13 ethambutol
aftB 4267243 p.Leu532Met missense_variant 0.17 capreomycin
amikacin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance