TB-Profiler result

Run: SRR13837687
Summary

Run ID: SRR13837687

Sample name:

Date: 2024-03-25T16:50:04.913315

Number of reads: 294748

Percentage reads mapped: 97.31

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 p.Ser424* 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 4326203 p.Ser424* stop_gained 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
gyrB 5532 c.295dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
gyrB 5832 p.Ala198Gly missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 6976 c.-326A>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
ccsA 620100 c.210G>T synonymous_variant 1.0 capreomycin
amikacin
kanamycin
rpoB 759609 c.-198C>A upstream_gene_variant 1.0 rifampicin Uncertain significance
mmpL5 776796 p.Val562Ala missense_variant 1.0 clofazimine
bedaquiline
mmpS5 778642 p.Trp88* stop_gained 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
inhA 1674891 p.Trp230Cys missense_variant 1.0 ethionamide
isoniazid
tlyA 1918625 p.Pro229Leu missense_variant 1.0 capreomycin
ndh 2103309 c.-267C>T upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
Rv1979c 2222721 c.444G>C synonymous_variant 1.0 clofazimine
bedaquiline
ahpC 2726345 p.Phe51Leu missense_variant 1.0 isoniazid
Rv2752c 3066881 c.-690C>A upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3067095 c.-904G>C upstream_gene_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
mtrB 3626528 p.Ala29Gly missense_variant 1.0 bedaquiline
rifampicin
alr 3840783 c.637_638insT frameshift_variant 1.0 cycloserine
panD 4044544 c.-263G>C upstream_gene_variant 1.0 pyrazinamide
embA 4242250 c.-983C>G upstream_gene_variant 1.0 ethambutol