TB-Profiler result

Run: ERR038738

Summary

Run ID: ERR038738

Sample name:

Date: 19-10-2023 17:59:03

Number of reads: 21925959

Percentage reads mapped: 99.58

Strain: lineage4.6.1.1

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 c.1312_1314delAAC (0.62), rpoB p.Ser450Leu (0.39)
Isoniazid
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide
Streptomycin R gid c.115delC (0.62)
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
lineage4.6.1.1 Euro-American T2-Uganda 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 761114 c.1312_1314delAAC conservative_inframe_deletion 0.62 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4408087 c.115delC frameshift_variant 0.62 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155295 p.Gly273Cys missense_variant 0.91
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
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407928 p.Glu92Gly missense_variant 0.17