TB-Profiler result

Run: SRR13837685
Summary

Run ID: SRR13837685

Sample name:

Date: 2024-10-04T02:22:49.133349

Number of reads: 293870

Percentage reads mapped: 97.01

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
gyrB 5832 p.Ala198Gly missense_variant 1.0 levofloxacin
moxifloxacin
rpoB 759609 c.-198C>A upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 763050 c.-320C>T upstream_gene_variant 1.0 rifampicin
mmpL5 776796 p.Val562Ala missense_variant 1.0 bedaquiline
clofazimine
tlyA 1918625 p.Pro229Leu missense_variant 1.0 capreomycin
ndh 2103309 c.-267C>T upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
Rv1979c 2222721 c.444G>C synonymous_variant 1.0 bedaquiline
clofazimine
ahpC 2726345 p.Phe51Leu missense_variant 1.0 isoniazid
Rv2752c 3067095 c.-904G>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv3083 3448912 p.Ile137Phe missense_variant 1.0 ethionamide
lpqB 3624303 p.Leu203Arg missense_variant 1.0 rifampicin
bedaquiline
mtrB 3626528 p.Ala29Gly missense_variant 1.0 rifampicin
bedaquiline
alr 3840783 c.637_638insT frameshift_variant 1.0 cycloserine
panD 4044544 c.-263G>C upstream_gene_variant 1.0 pyrazinamide
embC 4241026 c.1164C>G synonymous_variant 1.0 ethambutol
embA 4242250 c.-983C>G upstream_gene_variant 1.0 ethambutol
embB 4249328 p.Met939Leu missense_variant 1.0 ethambutol