TB-Profiler result

Run: ERR6866112
Summary

Run ID: ERR6866112

Sample name:

Date: 2024-04-16T12:49:54.576752

Number of reads: 1738471

Percentage reads mapped: 99.63

Median coverage: 53.0

Strain: lineage4.1.2.1;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
lineage4.3 Euro-American (LAM) None 0.2
lineage4.1 Euro-American None 0.34
lineage4.1.2 Euro-American None 0.35
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.29
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.22
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. 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
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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
inhA 1673423 c.-779G>T upstream_gene_variant 0.48 isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
katG 2155168 p.Ser315Thr missense_variant 0.23 isoniazid Assoc w R High-level resistance
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 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.98 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
mshA 575679 p.Asn111Ser missense_variant 0.48 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.29 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.35 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.38 rifampicin Not assoc w R
rpoB 761889 p.Val695Leu missense_variant 0.46 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.41 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.3 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.54 linezolid Not assoc w R - Interim
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.38 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.61 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.28 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.17 isoniazid
Rv2477c 2783921 p.Gly41Glu missense_variant 0.24 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Not assoc w R
amikacin Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 0.51 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 0.29 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.57 cycloserine
Rv3083 3448439 c.-64delA upstream_gene_variant 0.38 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 0.63 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641454 c.912G>A synonymous_variant 0.36 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.26 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.2 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.15 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 0.31 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 0.43 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407973 p.Val77Gly missense_variant 0.18 streptomycin Uncertain significance