TB-Profiler result

Run: ERR4829900
Summary

Run ID: ERR4829900

Sample name:

Date: 2024-10-03T20:10:11.736069

Number of reads: 3387175

Percentage reads mapped: 99.68

Median coverage: 107.0

Strain: lineage4.7;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 0.83
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.2
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 High-level resistance
ethambutol
pyrazinamide pncA c.-11A>G Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.18 pyrazinamide 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
dnaA 1126 c.1126C>T synonymous_variant 0.84 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7762 p.Pro154Leu missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781443 c.-117T>G upstream_gene_variant 0.88 streptomycin
Rv1258c 1407604 c.-264C>T upstream_gene_variant 0.86 streptomycin
pyrazinamide
isoniazid
embR 1416757 c.591G>A synonymous_variant 0.2 ethambutol Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155971 c.141A>G synonymous_variant 0.18 isoniazid Not assoc w R - Interim
PPE35 2168149 p.Pro822Ser missense_variant 0.15 pyrazinamide Not assoc w R
PPE35 2170675 c.-63G>C upstream_gene_variant 0.9 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pepQ 2859961 p.Ala153Gly missense_variant 0.74 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.23 capreomycin
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.22 ethionamide
mtrB 3626308 c.306T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3877547 p.Ala321Ser missense_variant 0.24 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.95 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R