TB-Profiler result

Run: SRR13837702
Summary

Run ID: SRR13837702

Sample name:

Date: 2024-10-04T05:49:42.251309

Number of reads: 295456

Percentage reads mapped: 98.55

Median coverage: 10.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
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
mshA 576327 p.Phe327Tyr missense_variant 1.0 isoniazid
ethionamide
Rv0565c 656192 p.Asp427His missense_variant 1.0 ethionamide
rpoB 760178 c.372G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764262 p.Val298Ala missense_variant 1.0 rifampicin
mmpL5 777280 p.Ala401Ser missense_variant 1.0 bedaquiline
clofazimine
rpsL 781277 c.-283G>C upstream_gene_variant 1.0 streptomycin
rplC 800213 c.-596G>T upstream_gene_variant 1.0 linezolid
embR 1416662 p.Arg229Pro missense_variant 1.0 ethambutol
rrl 1476288 n.2631T>C non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
tlyA 1917545 c.-395T>A upstream_gene_variant 1.0 capreomycin
Rv1979c 2222433 c.732A>G synonymous_variant 1.0 bedaquiline
clofazimine
Rv2681 2996821 p.Gly28Val missense_variant 1.0 capreomycin
ald 3086631 c.-189A>G upstream_gene_variant 1.0 cycloserine
Rv3236c 3612954 c.162delC frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3613619 c.-503T>G upstream_gene_variant 1.0 pyrazinamide
alr 3840284 p.Trp379* stop_gained 1.0 cycloserine
embC 4240042 p.Asn60Lys missense_variant 1.0 ethambutol
embB 4245806 c.-708G>A upstream_gene_variant 1.0 ethambutol
embB 4247075 c.563dupT frameshift_variant 1.0 ethambutol
embB 4249763 p.Thr1084Pro missense_variant 1.0 ethambutol Uncertain significance