TB-Profiler result

Run: ERR9786497
Summary

Run ID: ERR9786497

Sample name:

Date: 2024-04-15T00:16:56.216770

Number of reads: 884768

Percentage reads mapped: 99.72

Median coverage: 42.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.38
lineage4.1.2 Euro-American None 0.39
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.38
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.62
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 gid p.Glu24* Assoc w R
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
gid 4408133 p.Glu24* stop_gained 0.37 streptomycin Assoc w R
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 371 p.Pro124Leu missense_variant 0.75 isoniazid Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.41 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.41 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657033 p.Tyr146* stop_gained 0.4 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.22 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.41 rifampicin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.62 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.38 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2996288 p.Ala62Thr missense_variant 0.63 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.38 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.42 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840764 c.657G>C synonymous_variant 0.63 cycloserine
glpK 4138420 p.Asp446Tyr missense_variant 0.43 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.27 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.38 ethambutol Not assoc w R
embB 4248645 p.Ala711Asp missense_variant 0.71 ethambutol
whiB6 4338427 p.Gly32Ala missense_variant 0.6 capreomycin
amikacin
kanamycin
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 4338732 c.-211C>T upstream_gene_variant 0.36 capreomycin
amikacin
kanamycin