TB-Profiler result

Run: SRR12199427
Summary

Run ID: SRR12199427

Sample name:

Date: 2024-10-04T00:26:42.997950

Number of reads: 264624

Percentage reads mapped: 50.69

Median coverage: 6.0

Strain: lineage1.2.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.5
lineage1 Indo-Oceanic RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic RD239 0.53
lineage1.2.1 Indo-Oceanic RD239 0.54
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
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0 streptomycin Not assoc w R
pyrazinamide Not assoc w R
isoniazid Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
atpE 1460907 c.-138T>C upstream_gene_variant 1.0 bedaquiline
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568488 c.191delG frameshift_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
alr 3841546 c.-126C>A upstream_gene_variant 0.42 cycloserine
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269864 c.-32delG upstream_gene_variant 1.0 ethambutol Not assoc w R