TB-Profiler result

Run: ERR1034581

Summary

Run ID: ERR1034581

Sample name:

Date: 20-10-2023 21:59:59

Number of reads: 16559328

Percentage reads mapped: 99.46

Strain: lineage3.1.2

Drug-resistance: Pre-XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Asp435Val (1.00)
Isoniazid R katG p.Ser315Asn (1.00)
Ethambutol R embB p.Asp1024Asn (1.00)
Pyrazinamide R pncA p.Ala146Glu (0.13), pncA c.390_391dupGG (0.87), pncA c.390_391dupGG (0.87)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.87), gyrA p.Asp94Gly (0.11)
Moxifloxacin R gyrA p.Ala90Val (0.87), gyrA p.Asp94Gly (0.11)
Ofloxacin R gyrA p.Ala90Val (0.87), gyrA p.Asp94Gly (0.11)
Levofloxacin R gyrA p.Ala90Val (0.87), gyrA p.Asp94Gly (0.11)
Ciprofloxacin R gyrA p.Ala90Val (0.87), gyrA p.Asp94Gly (0.11)
Aminoglycosides R rrs n.1401A>G (0.85)
Amikacin R rrs n.1401A>G (0.85)
Capreomycin R rrs n.1401A>G (0.85)
Kanamycin R rrs n.1401A>G (0.85)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
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
gyrA 7570 p.Ala90Val missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.85 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 0.13 pyrazinamide
pncA 2288850 c.390_391dupGG frameshift_variant 0.87 pyrazinamide, pyrazinamide
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576183 p.Ala279Val missense_variant 0.26
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474878 p.Arg291His missense_variant 1.0
fprA 3475052 p.Asn349Thr missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267671 p.Ala389Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0