TB-Profiler result

Run: SRR12199397
Summary

Run ID: SRR12199397

Sample name:

Date: 2024-03-26T19:16:16.323424

Number of reads: 298593

Percentage reads mapped: 98.41

Median coverage: 6.0

Strain: lineage1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 0.97
lineage1 Indo-Oceanic RD239 0.97
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 fbiD c.-10265_*5816del 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
fbiD 3328852 c.-10265_*5816del transcript_ablation 0.92 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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2169901 p.Gly238Trp missense_variant 0.85 pyrazinamide Uncertain significance
PPE35 2170649 c.-37T>G upstream_gene_variant 0.71 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.78 ethambutol Not assoc w R