TB-Profiler result

Run: ERR038740

Summary

Run ID: ERR038740

Sample name:

Date: 19-10-2023 17:59:45

Number of reads: 21103928

Percentage reads mapped: 99.5

Strain: lineage4.6.1.2

Drug-resistance: MDR-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.His445Cys (1.00)
Isoniazid R ahpC c.-57C>T (1.00)
Ethambutol
Pyrazinamide R pncA c.340_346dupACGCCAC (0.97)
Streptomycin R gid c.102delG (0.99)
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 761139 p.His445Cys missense_variant 1.0 rifampicin
pncA 2288895 c.340_346dupACGCCAC frameshift_variant 0.97 pyrazinamide
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid
gid 4408100 c.102delG frameshift_variant 0.99 streptomycin
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154834 p.Tyr426* stop_gained 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-42_-40delCAT upstream_gene_variant 1.0
embA 4243709 c.477C>T synonymous_variant 0.99
embA 4245055 p.Thr608Asn missense_variant 1.0
ubiA 4269148 p.Val229Ala missense_variant 0.99
ethA 4326405 p.Asp357Tyr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0