TB-Profiler result

Run: SRR26159054
Summary

Run ID: SRR26159054

Sample name:

Date: 2024-04-15T03:57:25.589661

Number of reads: 916511

Percentage reads mapped: 99.58

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level 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
fabG1 1673770 p.Ala111Pro missense_variant 0.52 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99 isoniazid
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248015 p.Thr501Met missense_variant 1.0 ethambutol
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407734 p.Gly157Arg missense_variant 1.0 streptomycin Uncertain significance
gid 4407780 c.423G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R