TB-Profiler result

Run: SRR13837690
Summary

Run ID: SRR13837690

Sample name:

Date: 2024-04-14T13:00:34.387888

Number of reads: 293810

Percentage reads mapped: 96.01

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 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
dnaA 1057 p.Val353Leu missense_variant 1.0 isoniazid Uncertain significance
gyrB 5532 c.295dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
ccsA 619735 c.-156G>C upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
rpoC 763050 c.-320C>T upstream_gene_variant 1.0 rifampicin
mmpL5 776796 p.Val562Ala missense_variant 1.0 clofazimine
bedaquiline
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
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
Rv3083 3448912 p.Ile137Phe missense_variant 1.0 ethionamide
whiB7 3568676 p.Ser2Ala missense_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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
glpK 4138911 p.Gly282Val missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
aftB 4267490 c.1347G>C synonymous_variant 1.0 ethambutol