TB-Profiler result

Run: 6577abf7-6645-434b-971e-70e6c7835e82
Summary

Run ID: 6577abf7-6645-434b-971e-70e6c7835e82

Sample name:

Date: 13-02-2023 07:52:00

Number of reads: 272856

Percentage reads mapped: 98.98

Median coverage: 13

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG c.1402delA Uncertain significance
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
katG 2154709 c.1402delA frameshift_variant 0.12 isoniazid Uncertain significance
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 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 8040 p.Gly247Ser missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
rpoC 763754 p.Ile129Val missense_variant 0.18 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin
rpoC 765847 p.Asn826Lys missense_variant 1.0 rifampicin
rpoC 766355 p.Gly996Ser missense_variant 0.12 rifampicin
rpoC 766429 c.3062dupG frameshift_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777214 p.Ala423Thr missense_variant 0.13 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
fabG1 1673936 p.Ser166* stop_gained 0.11 ethionamide
isoniazid
rpsA 1834513 c.972C>G synonymous_variant 1.0 pyrazinamide
katG 2154246 c.1866T>C synonymous_variant 0.1 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2290023 c.-782A>T upstream_gene_variant 0.12 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
eis 2714865 c.468C>A synonymous_variant 0.2 kanamycin
amikacin
eis 2714923 p.Leu137Trp missense_variant 0.13 kanamycin
amikacin
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0 rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087310 p.Pro164Leu missense_variant 0.12 cycloserine
ald 3087665 c.847delT frameshift_variant 0.17 cycloserine
Rv3083 3449860 p.Arg453Cys missense_variant 1.0 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide
clpC1 4040445 p.Val87Asp missense_variant 0.1 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4244184 p.Ser318Leu missense_variant 0.12 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Uncertain significance