TB-Profiler result

Run: SRR29096170
Summary

Run ID: SRR29096170

Sample name:

Date: 2025-02-11T17:31:23.712414

Number of reads: 307864

Percentage reads mapped: 92.09

Median coverage: 9.0

Strain: lineage4.4.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1.2 Euro-American None 0.99
lineage4.4.1 Euro-American (S-type) None 0.99
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
nusG 734451 c.198G>C synonymous_variant 0.5 rifampicin
nusG 734457 c.204C>G synonymous_variant 0.5 rifampicin
nusG 734472 c.219T>C synonymous_variant 0.55 rifampicin
nusG 734475 c.222T>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
nusG 734532 c.279A>G synonymous_variant 0.57 rifampicin Not assoc w R - Interim
nusG 734556 c.303C>T synonymous_variant 0.5 rifampicin
nusG 734559 c.306T>C synonymous_variant 0.55 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 0.3 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 762293 c.2487T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 765019 c.1650A>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 765034 c.1665T>C synonymous_variant 0.44 rifampicin
rpoC 765734 c.2365T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.43 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.44 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.44 rifampicin Uncertain significance
rpoC 765772 c.2403C>G synonymous_variant 0.5 rifampicin
rpoC 765784 c.2415C>G synonymous_variant 0.57 rifampicin
rpoC 765787 c.2418C>T synonymous_variant 0.54 rifampicin
rpoC 765793 c.2424C>G synonymous_variant 0.47 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 0.46 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpsL 781929 p.Gly124Ser missense_variant 0.35 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2167770 p.Ser948Ile missense_variant 1.0 pyrazinamide Not assoc w R
pepQ 2860213 p.Pro69Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R