TB-Profiler result

Run: SRR13837908
Summary

Run ID: SRR13837908

Sample name:

Date: 2025-03-04T21:49:47.237572

Number of reads: 2936430

Percentage reads mapped: 100.0

Median coverage: 100.0

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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fgd1 p.Lys259* 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
fgd1 491557 p.Lys259* stop_gained 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-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
dnaA 1509 p.Gln503His missense_variant 1.0 isoniazid Uncertain significance
gyrB 5417 p.Gly60Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6381 p.Lys381Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491364 c.582T>C synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv0565c 657034 p.Tyr146Cys missense_variant 1.0 ethionamide Uncertain significance
rpoB 759579 c.-228G>A upstream_gene_variant 1.0 rifampicin Uncertain significance
sigE 1364881 p.Glu157Lys missense_variant 1.0 pyrazinamide Uncertain significance
Rv1258c 1406579 c.762C>T synonymous_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrl 1473445 n.-213G>T upstream_gene_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475387 n.1730C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673735 c.-467G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674246 c.45C>T synonymous_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674937 c.736C>T synonymous_variant 0.99 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833345 c.-196delC upstream_gene_variant 1.0 pyrazinamide Uncertain significance
tsnR 1853672 c.70delG frameshift_variant 1.0 linezolid Uncertain significance
PPE35 2170775 c.-163T>A upstream_gene_variant 1.0 pyrazinamide Uncertain significance
pncA 2289663 c.-422A>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
pncA 2290143 c.-903_-902insG upstream_gene_variant 1.0 pyrazinamide Uncertain significance
eis 2714984 p.Ala117Thr missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726534 c.342C>T synonymous_variant 1.0 isoniazid Uncertain significance
thyA 3074240 p.Thr78Ser missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
ald 3086806 c.-14_-13insA upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448862 p.Gly120Ala missense_variant 1.0 ethionamide Uncertain significance
alr 3840667 p.Arg252Gly missense_variant 1.0 cycloserine Uncertain significance
rpoA 3878142 c.366C>G synonymous_variant 1.0 rifampicin Uncertain significance
clpC1 4040117 p.Glu196Asp missense_variant 1.0 pyrazinamide Uncertain significance
embA 4242988 c.-245A>G upstream_gene_variant 1.0 ethambutol Uncertain significance
ubiA 4269624 p.Tyr70* stop_gained 1.0 ethambutol Uncertain significance
ethR 4328039 p.Arg164Pro missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338235 p.Arg96Leu missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance