TB-Profiler result

Run: ERR1750941
Summary

Run ID: ERR1750941

Sample name:

Date: 2024-04-16T09:20:36.232181

Number of reads: 1463975

Percentage reads mapped: 95.3

Median coverage: 45.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.84
lineage4.1.2 Euro-American None 0.75
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.56
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.11
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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
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 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.72 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.76 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.64 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 0.79 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.71 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2715436 c.-104G>A upstream_gene_variant 1.0 amikacin
kanamycin
clpC1 4039729 p.Asp326Asn missense_variant 0.5 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.86 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 0.92 ethambutol Not assoc w R
aftB 4268384 p.Leu151Phe missense_variant 0.59 ethambutol Uncertain significance
ubiA 4270009 c.-176C>T upstream_gene_variant 0.39 ethambutol