TB-Profiler result

Run: SRR13837662
Summary

Run ID: SRR13837662

Sample name:

Date: 2024-10-05T04:58:17.760439

Number of reads: 293831

Percentage reads mapped: 98.01

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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.905delT Assoc w R
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
ethA 4326568 c.905delT frameshift_variant 1.0 ethionamide 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
gyrA 8820 p.Asp507His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 575967 p.Val207Asp missense_variant 1.0 isoniazid
ethionamide
rpoB 759961 p.Thr52Asn missense_variant 1.0 rifampicin
rpoB 763050 p.Leu1082Met missense_variant 1.0 rifampicin
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0 bedaquiline
clofazimine
Rv1129c 1253966 p.Leu190Trp missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
fbiC 1304512 p.Val528Ile missense_variant 1.0 pretomanid
delamanid
clofazimine
embR 1417704 c.-357T>C upstream_gene_variant 0.92 ethambutol
whiB7 3568679 p.Val1Leu missense_variant 1.0 kanamycin
amikacin
streptomycin
clpC1 4040066 c.639G>T synonymous_variant 1.0 pyrazinamide
embC 4241259 c.1397_1398insT frameshift_variant 0.92 ethambutol
embA 4243358 c.126C>T synonymous_variant 1.0 ethambutol
embB 4248436 c.1923C>T synonymous_variant 1.0 ethambutol
ubiA 4269557 p.Ala93Pro missense_variant 1.0 ethambutol