TB-Profiler result

Run: a428d6c6-88f3-414c-80a9-0c99e9fc7c12
Summary

Run ID: a428d6c6-88f3-414c-80a9-0c99e9fc7c12

Sample name:

Date: 25-06-2023 06:50:09

Number of reads: 289374

Percentage reads mapped: 98.95

Median coverage: 8

Strain: lineage3.1.1

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 0.99
lineage3.1 East-African-Indian RD750 1.0
lineage3.1.1 East-African-Indian RD750 1.0
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
gyrB 5438 p.Val67Leu missense_variant 0.15 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 5820 p.Leu194Pro missense_variant 0.17 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6977 p.Phe580Leu missense_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9080 c.1779G>A synonymous_variant 0.18 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 491768 p.Ala329Glu missense_variant 0.18 delamanid
mshA 575605 c.258G>T synonymous_variant 0.18 ethionamide
isoniazid
rpoB 760264 p.Met153Lys missense_variant 0.18 rifampicin
rpoB 762106 c.2303dupC frameshift_variant 0.2 rifampicin
rpoB 762312 p.Gly836Ser missense_variant 0.12 rifampicin Uncertain significance
rpoC 762434 c.-936T>G upstream_gene_variant 1.0 rifampicin
mmpL5 776659 p.Asp608Asn missense_variant 0.12 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 778351 p.Ala44Thr missense_variant 0.2 clofazimine
bedaquiline
mmpL5 778507 c.-27C>A upstream_gene_variant 0.18 clofazimine
bedaquiline
mmpS5 778652 p.Ala85Val missense_variant 0.17 clofazimine
bedaquiline
rrs 1472517 n.672T>C non_coding_transcript_exon_variant 0.11 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473089 n.1244A>G non_coding_transcript_exon_variant 0.14 linezolid
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
aminoglycosides
streptomycin
rrl 1474509 n.852G>T non_coding_transcript_exon_variant 0.2 linezolid
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.15 linezolid
rrl 1476224 n.2567A>T non_coding_transcript_exon_variant 0.18 linezolid
inhA 1674868 p.Asp223Asn missense_variant 0.15 ethionamide
isoniazid
rpsA 1834142 p.Glu201* stop_gained 0.17 pyrazinamide
ndh 2102510 c.532delG frameshift_variant 0.15 ethionamide
isoniazid
katG 2154089 p.Asp675Asn missense_variant 0.12 isoniazid
PPE35 2168044 p.Ala857Ser missense_variant 0.2 pyrazinamide
PPE35 2168348 c.2265T>C synonymous_variant 0.2 pyrazinamide
PPE35 2170461 p.Gly51Glu missense_variant 1.0 pyrazinamide
Rv1979c 2222179 p.Ala329Val missense_variant 0.17 clofazimine
bedaquiline
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide
ahpC 2725958 c.-235C>A upstream_gene_variant 0.11 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
thyA 3074133 c.339C>T synonymous_variant 0.17 para-aminosalicylic_acid
thyA 3074211 c.261A>T synonymous_variant 0.17 para-aminosalicylic_acid
fbiA 3640911 p.Tyr123* stop_gained 0.15 delamanid
alr 3841615 c.-195T>C upstream_gene_variant 0.11 cycloserine
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243409 c.177C>T synonymous_variant 0.15 ethambutol
embB 4246548 p.Pro12Gln missense_variant 0.15 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.18 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.18 ethambutol Uncertain significance
embB 4247632 c.1119C>A synonymous_variant 0.17 ethambutol
aftB 4268876 c.-40G>A upstream_gene_variant 0.17 capreomycin
amikacin Uncertain significance
ethA 4326657 p.Pro273Thr missense_variant 0.14 ethionamide
ethR 4327618 p.Asp24Asn missense_variant 0.14 ethionamide
ethA 4328322 c.-850_-849insT upstream_gene_variant 0.18 ethionamide
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