TB-Profiler result

Run: ERR987753
Summary

Run ID: ERR987753

Sample name:

Date: 2024-04-16T05:19:25.778977

Number of reads: 13176850

Percentage reads mapped: 99.44

Median coverage: 229.0

Strain: lineage3;lineage4.2;lineage4.6.1.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.81
lineage4.6 Euro-American None 0.11
lineage4.2 Euro-American None 0.05
lineage4.6.1.2 Euro-American RD724 0.11
lineage4 Euro-American None 0.18
lineage4.6.1 Euro-American (Uganda) RD724 0.11
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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 0.11 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid Assoc w R High-level resistance
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574900 c.-448G>C upstream_gene_variant 0.78 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 0.77 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.82 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 0.82 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
rplC 800204 c.-605T>C upstream_gene_variant 0.12 linezolid
Rv1129c 1253541 p.Ile332Leu missense_variant 0.8 moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.84 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254591 c.-57C>T upstream_gene_variant 0.81 moxifloxacin
levofloxacin
rifampicin
isoniazid
embR 1416410 p.Leu313Arg missense_variant 0.11 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476758 n.3101G>C non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
fabG1 1673152 c.-288A>G upstream_gene_variant 0.14 ethionamide
isoniazid
inhA 1674465 c.264C>T synonymous_variant 0.16 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.81 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 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 0.82 pyrazinamide
kasA 2518586 p.Leu158Phe missense_variant 0.1 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.85 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.8 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
Rv2681 2996876 c.138A>C synonymous_variant 0.1 capreomycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.91 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.12 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.83 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642098 c.564G>A synonymous_variant 0.77 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
alr 3840636 p.Pro262Gln missense_variant 0.8 cycloserine
rpoA 3878622 c.-115C>G upstream_gene_variant 0.88 rifampicin Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 0.17 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.74 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.11 ethambutol Uncertain significance
embA 4245883 p.Gly884Asp missense_variant 0.8 ethambutol Uncertain significance
ethA 4326230 p.Asp415Gly missense_variant 0.83 ethionamide 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 4338635 c.-114A>C upstream_gene_variant 0.1 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.81 streptomycin Not assoc w R