TB-Profiler result

Run: ERR2707074
Summary

Run ID: ERR2707074

Sample name:

Date: 19-10-2023 12:09:29

Number of reads: 2882009

Percentage reads mapped: 99.65

Strain: lineage4.6.1.2

Drug-resistance: RR-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.Ser450Leu (1.00)
Isoniazid
Ethambutol R embA c.-11C>A (1.00), embB p.Met306Ile (0.35)
Pyrazinamide
Streptomycin R rrs n.905C>G (0.64)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472750 n.905C>G non_coding_transcript_exon_variant 0.64 streptomycin
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.35 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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762127 p.Val774Glu missense_variant 0.33
rpoC 764810 p.Pro481Thr missense_variant 1.0
rpoC 765862 p.Phe831Leu missense_variant 0.59
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155249 p.Pro288His missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289010 p.Gly78Arg missense_variant 1.0
Rv2752c 3065920 p.Pro91Leu missense_variant 1.0
Rv2752c 3066211 c.-20A>G upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
ubiA 4269148 p.Val229Ala missense_variant 0.68
whiB6 4338595 c.-75delG upstream_gene_variant 1.0