TB-Profiler result

Run: ERR6197031
Summary

Run ID: ERR6197031

Sample name:

Date: 2024-04-16T12:48:24.420844

Number of reads: 1384091

Percentage reads mapped: 95.15

Median coverage: 44.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 0.99
lineage4 Euro-American 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
dnaA 1126 c.1126C>T synonymous_variant 0.94 isoniazid Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 762989 c.-381G>C upstream_gene_variant 0.18 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763005 p.Cys1067Val missense_variant 0.18 rifampicin
rpoC 763013 c.-357C>A upstream_gene_variant 0.15 rifampicin
rpoC 763022 c.-348C>A upstream_gene_variant 0.15 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763052 c.-318G>C upstream_gene_variant 0.15 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763074 p.Thr1090Val missense_variant 0.14 rifampicin
rpoB 763085 c.3279C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763103 c.-267G>A upstream_gene_variant 0.12 rifampicin
rpoC 763109 c.-261C>G upstream_gene_variant 0.1 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781443 c.-117T>G upstream_gene_variant 1.0 streptomycin
Rv1258c 1407604 c.-264C>T upstream_gene_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.97 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2170675 c.-63G>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pepQ 2859961 p.Ala153Gly missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R