TB-Profiler result

Run: 88752c56-7255-4be7-9661-a03e8dfb88d3
Summary

Run ID: 88752c56-7255-4be7-9661-a03e8dfb88d3

Sample name:

Date: 02-04-2024 16:17:40

Number of reads: 433341

Percentage reads mapped: 80.4

Median coverage: 11

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 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 fabG1 c.-15C>T Assoc w R
katG p.Ser315Thr Assoc w R
ethambutol embA c.-12C>T Assoc w R
embB p.Tyr334His Uncertain significance
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rpsL p.Lys88Arg Assoc w R
amikacin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
clofazimine
ethionamide fabG1 c.-15C>T Assoc w R
para-aminosalicylic_acid
cycloserine
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
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.94 kanamycin Assoc w R
capreomycin Assoc w R
aminoglycosides Uncertain significance
amikacin Assoc w R
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid Assoc w R
ethionamide Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Assoc w R
embB 4247513 p.Tyr334His missense_variant 1.0 ethambutol Uncertain significance
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775871 c.2610C>T synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 775874 c.2607C>A synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473314 n.1469A>C non_coding_transcript_exon_variant 0.11 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19 ethionamide
isoniazid
Rv1979c 2221894 p.Val424Gly missense_variant 0.14 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086997 p.Thr60Gly missense_variant 0.17 cycloserine
ald 3087532 p.Ala238Asp missense_variant 1.0 cycloserine
Rv3236c 3612229 c.888C>T synonymous_variant 1.0 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.3 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.3 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.2 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.2 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
ethA 4326975 p.Trp167Arg missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance