TB-Profiler result

Run: da419f21-70db-4d11-9015-c5964c50c7eb
Summary

Run ID: da419f21-70db-4d11-9015-c5964c50c7eb

Sample name:

Date: 01-05-2024 20:29:03

Number of reads: 1882822

Percentage reads mapped: 98.99

Median coverage: 59

Strain: lineage3.1.2.1

Spoligotype:

Drug-resistance: MDR-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 0.99
lineage3.1 East-African-Indian RD750 0.97
lineage3.1.2 East-African-Indian RD750 0.99
lineage3.1.2.1 East-African-Indian RD750 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rrs n.517C>T Assoc w R
amikacin
kanamycin
capreomycin
clofazimine
ethionamide ethA c.1242delT Assoc w R - interim
c.1242delT Uncertain significance
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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol Assoc w R
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide Assoc w R - interim
ethionamide Uncertain significance
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 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 0.98 delamanid
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 762434 c.-936T>G upstream_gene_variant 1.0 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2154724 p.Arg463Leu missense_variant 0.98 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168604 p.Pro670Leu missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
eis 2714401 p.Ala311Val missense_variant 0.99 kanamycin
amikacin
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
ubiA 4269298 p.Ile179Thr missense_variant 0.98 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin