TB-Profiler result

Run: SRR13837875
Summary

Run ID: SRR13837875

Sample name:

Date: 2025-03-05T15:18:30.076534

Number of reads: 2936527

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 fbiC c.170dupA Assoc w R - Interim Confers DLM-PMD cross-resistance
c.1116delC 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 1303099 c.170dupA frameshift_variant 0.99 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiC 1304043 c.1116delC frameshift_variant 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
gyrA 9490 p.Gly730Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13883 c.-325T>A upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491231 p.Phe150Tyr missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv0565c 656020 p.Gly484Val missense_variant 1.0 ethionamide Uncertain significance
rpoC 766128 p.Ala920Gly missense_variant 1.0 rifampicin Uncertain significance
rpsL 781503 c.-57T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800381 c.-428A>G upstream_gene_variant 1.0 linezolid Uncertain significance
sigE 1364655 p.Met81Ile missense_variant 1.0 pyrazinamide Uncertain significance
Rv1258c 1406861 p.Ile160Met missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
Rv1258c 1407463 c.-123G>C upstream_gene_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1472303 n.458G>A non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474235 n.578G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475139 n.1482C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476248 n.2591G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476576 n.2919C>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
bacA 2063299 p.Trp477Leu missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
kasA 2518209 p.Thr32Arg missense_variant 1.0 isoniazid Uncertain significance
folC 2746788 p.Ala271Pro missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyX 3067214 p.Ser244Arg missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
fbiD 3339396 c.279C>T synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mtrA 3627293 p.Glu19Asp missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3878048 p.Ala154Ser missense_variant 1.0 rifampicin Uncertain significance
panD 4044922 c.-641G>T upstream_gene_variant 1.0 pyrazinamide Uncertain significance
glpK 4139628 p.Gln43Leu missense_variant 0.99 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embB 4248368 p.Leu619Val missense_variant 1.0 ethambutol Uncertain significance
ethA 4327082 p.Cys131Ser missense_variant 1.0 ethionamide Uncertain significance
ethA 4327097 p.Leu126His missense_variant 1.0 ethionamide Uncertain significance
gid 4407792 c.411G>C synonymous_variant 1.0 streptomycin Uncertain significance