TB-Profiler result

Run: ERR228213
Summary

Run ID: ERR228213

Sample name:

Date: 2024-04-14T02:08:38.696069

Number of reads: 3137823

Percentage reads mapped: 99.34

Median coverage: 70.0

Strain: lineage3;lineage4

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.85
lineage4 Euro-American None 0.18
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 rpsL p.Lys43Arg 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
rpsL 781687 p.Lys43Arg missense_variant 0.14 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.87 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13250 c.309G>A synonymous_variant 0.8 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574900 c.-448G>C upstream_gene_variant 0.8 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.86 ethionamide Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.87 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.81 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 1254131 p.Glu135Ala missense_variant 0.72 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.87 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364202 c.-211G>A upstream_gene_variant 0.16 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.81 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063999 p.Val244Met missense_variant 0.77 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.92 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.91 pyrazinamide 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
pncA 2289365 c.-125delC upstream_gene_variant 0.91 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.84 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.85 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.9 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.88 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642098 c.564G>A synonymous_variant 0.7 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
alr 3840636 p.Pro262Gln missense_variant 0.86 cycloserine
rpoA 3878622 c.-115C>G upstream_gene_variant 0.74 rifampicin Uncertain significance
embC 4239332 c.-531C>A upstream_gene_variant 0.84 ethambutol Uncertain significance
embC 4241335 p.Gln491His missense_variant 0.72 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.91 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245883 p.Gly884Asp missense_variant 0.75 ethambutol Uncertain significance
embB 4248561 p.Ala683Val missense_variant 0.83 ethambutol Uncertain significance
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 0.94 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.87 streptomycin Not assoc w R