TB-Profiler result

Run: SRR18911120
Summary

Run ID: SRR18911120

Sample name:

Date: 2024-04-14T03:32:35.459303

Number of reads: 141299

Percentage reads mapped: 96.33

Median coverage: 4.0

Strain: lineage1.2.1.2.1;lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.15
lineage1 Indo-Oceanic RD239 0.47
lineage1.2.1.2.1 Indo-Oceanic RD239 0.16
lineage1.2.1 Indo-Oceanic RD239 0.11
lineage4.9 Euro-American (H37Rv-like) None 0.84
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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
atpE 1460907 c.-138T>C upstream_gene_variant 1.0 bedaquiline
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim