TB-Profiler result

Run: SRR13837684
Summary

Run ID: SRR13837684

Sample name:

Date: 2024-10-04T05:49:40.811442

Number of reads: 296593

Percentage reads mapped: 97.91

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
rpoB 760652 c.846C>A synonymous_variant 0.92 rifampicin
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781149 c.-411C>T upstream_gene_variant 0.92 streptomycin
rpsL 781277 c.-283G>T upstream_gene_variant 1.0 streptomycin
rrl 1473740 n.83G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
pncA 2289887 c.-646A>C upstream_gene_variant 1.0 pyrazinamide
Rv2477c 2783316 p.Thr243Ala missense_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
fbiD 3338954 c.-164A>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
lpqB 3624203 c.708C>T synonymous_variant 1.0 rifampicin
bedaquiline
glpK 4139747 p.Asp3Glu missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embA 4243843 c.613dupG frameshift_variant 1.0 ethambutol Uncertain significance
embA 4244833 p.Val534Ala missense_variant 1.0 ethambutol
aftB 4267994 p.Met281Ile missense_variant 1.0 ethambutol