TB-Profiler result

Run: ERR4797427
Summary

Run ID: ERR4797427

Sample name:

Date: 2024-04-15T04:31:48.014244

Number of reads: 2825660

Percentage reads mapped: 99.81

Median coverage: 66.0

Strain: lineage3;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
lineage3 East-African-Indian RD750 0.15
lineage4 Euro-American None 0.83
lineage4.8 Euro-American (mainly T) RD219 0.85
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575424 p.Arg26His missense_variant 0.11 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.71 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.78 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.28 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 0.37 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
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062978 p.Gly584Glu missense_variant 0.82 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2064373 p.Arg119Gln missense_variant 0.78 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.27 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.76 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
Rv2477c 2783066 p.His326Arg missense_variant 0.78 ethambutol Uncertain significance
moxifloxacin
streptomycin
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.84 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.24 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.76 pyrazinamide Not assoc w R
rpoA 3878804 c.-297G>T upstream_gene_variant 0.88 rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.81 pyrazinamide Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.18 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.26 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 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
gid 4407588 c.615A>G synonymous_variant 0.21 streptomycin Not assoc w R