TB-Profiler result

Run: aeee4575-59b1-4077-b997-48033ff4d08b
Summary

Run ID: aeee4575-59b1-4077-b997-48033ff4d08b

Sample name:

Date: 16-02-2023 09:19:37

Number of reads: 4350068

Percentage reads mapped: 99.04

Median coverage: 123

Strain: lineage3

Spoligotype:

Drug-resistance: Pre-XDR-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
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid fabG1 c.-17G>T Uncertain significance
katG p.Ser315Thr Assoc w R
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
moxifloxacin gyrA p.Asp94Asn Assoc w R
levofloxacin gyrA p.Asp94Asn Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rrs n.906A>G Uncertain significance
amikacin
kanamycin
capreomycin
clofazimine
ethionamide fabG1 c.-17G>T 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
gyrA 7581 p.Asp94Asn missense_variant 1.0 ofloxacin Uncertain significance
moxifloxacin Assoc w R
levofloxacin Assoc w R
fluoroquinolones Uncertain significance
ciprofloxacin Uncertain significance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol 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 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 1.0 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
rpoC 764916 p.Leu516Pro missense_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
rplC 800702 c.-107G>T upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1303644 c.714G>A synonymous_variant 0.98 delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474946 n.1289C>A non_coding_transcript_exon_variant 0.18 linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2154429 c.1683C>T synonymous_variant 1.0 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.98 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
kasA 2518863 p.Thr250Met missense_variant 1.0 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97 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
whiB7 3568857 c.-178C>T upstream_gene_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
amikacin Uncertain significance
alr 3840272 c.1149C>T synonymous_variant 1.0 cycloserine
panD 4044023 c.259C>T synonymous_variant 1.0 pyrazinamide
embC 4240546 c.684G>A synonymous_variant 1.0 ethambutol
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243204 c.-28delT upstream_gene_variant 1.0 ethambutol Uncertain significance
ethA 4326743 p.Leu244Pro missense_variant 0.42 ethionamide 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
gid 4407631 c.571delT frameshift_variant 1.0 streptomycin