TB-Profiler result

Run: SRR13837673
Summary

Run ID: SRR13837673

Sample name:

Date: 2024-10-04T09:41:47.739578

Number of reads: 293816

Percentage reads mapped: 95.0

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) None 1.0
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 pncA p.Val7Leu Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.827dupC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1303756 c.827dupC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pncA 2289223 p.Val7Leu missense_variant 1.0 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
mmaA3 737500 p.Ile217Ser missense_variant 0.92 isoniazid
mmaA3 738175 c.-26A>C upstream_gene_variant 1.0 isoniazid
rpoB 762083 c.2277T>A synonymous_variant 1.0 rifampicin
rpoC 766578 p.Asp1070Val missense_variant 1.0 rifampicin
kasA 2518058 c.-57G>A upstream_gene_variant 1.0 isoniazid
whiB7 3568660 p.Pro7Leu missense_variant 1.0 kanamycin
amikacin
streptomycin Uncertain significance
lpqB 3623509 p.Val468Ile missense_variant 1.0 rifampicin Uncertain significance
bedaquiline
mtrA 3627016 p.Leu112Val missense_variant 1.0 rifampicin
bedaquiline
alr 3841536 c.-117_-116insT upstream_gene_variant 1.0 cycloserine
ddn 3986940 p.Asp33His missense_variant 1.0 pretomanid
delamanid
panD 4045249 c.-968C>G upstream_gene_variant 1.0 pyrazinamide