TB-Profiler result

Run: cb11ac17-8130-4b0f-859c-5cff52b24d55
Summary

Run ID: cb11ac17-8130-4b0f-859c-5cff52b24d55

Sample name:

Date: 08-06-2023 01:32:05

Number of reads: 234719

Percentage reads mapped: 95.34

Median coverage: 5

Strain: lineage1.2.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1 Indo-Oceanic RD239 1.0
lineage1.2.1 Indo-Oceanic RD239 1.0
lineage1.2.1.2 Indo-Oceanic RD239 0.98
lineage1.2.1.2.1 Indo-Oceanic RD239 0.96
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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
para-aminosalicylic_acid
cycloserine
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 9009 p.Phe570Ile missense_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
rpoB 762510 p.Ala902Thr missense_variant 0.2 rifampicin
rpoC 763393 p.Asp8Glu missense_variant 0.2 rifampicin
mmpL5 776050 p.Ser811Pro missense_variant 0.15 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
fbiC 1302821 c.-110G>A upstream_gene_variant 1.0 delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rpsA 1834859 p.Ala440Thr missense_variant 0.14 pyrazinamide
katG 2154310 p.Gly601Asp missense_variant 0.18 isoniazid Uncertain significance
PPE35 2169828 p.Ala262Val missense_variant 0.15 pyrazinamide
PPE35 2169841 p.Gly258Ser missense_variant 0.15 pyrazinamide
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0 delamanid
alr 3840582 p.Ala280Val missense_variant 0.18 cycloserine
alr 3840762 p.Ala220Gly missense_variant 0.13 cycloserine
alr 3841443 c.-23G>T upstream_gene_variant 0.17 cycloserine
clpC1 4038768 p.Arg646Leu missense_variant 0.2 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Uncertain significance
embC 4239893 p.Ala11Pro missense_variant 0.2 ethambutol
embA 4244712 p.Ala494Leu missense_variant 0.13 ethambutol
embB 4248059 p.Gln516* stop_gained 0.15 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
ethR 4327649 p.Glu34Val missense_variant 0.2 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance