TB-Profiler result

Run: ERR11050120
Summary

Run ID: ERR11050120

Sample name:

Date: 2024-04-15T13:14:47.005717

Number of reads: 2346235

Percentage reads mapped: 99.86

Median coverage: 65.0

Strain: lineage4.7;lineage4.8

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 0.22
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.77
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 377 p.Thr126Ile missense_variant 0.32 isoniazid
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13711 c.-153C>T upstream_gene_variant 0.19 isoniazid Uncertain significance
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
Rv1129c 1253554 c.981G>C synonymous_variant 0.76 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1253865 p.Thr224Ala missense_variant 0.76 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2170530 p.Ala28Glu missense_variant 0.73 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2746922 p.Gly226Val missense_variant 0.43 para-aminosalicylic_acid
Rv2477c 2782776 c.1267C>A synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
fbiD 3339393 c.276G>A synonymous_variant 0.29 clofazimine
pretomanid
delamanid
embC 4239809 c.-54C>T upstream_gene_variant 0.8 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.22 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338710 c.-189A>T upstream_gene_variant 0.28 capreomycin
amikacin
kanamycin
whiB6 4338863 c.-342C>G upstream_gene_variant 0.73 capreomycin
amikacin
kanamycin