TB-Profiler result

Run: ERR3335745

Summary

Run ID: ERR3335745

Sample name:

Date: 21-10-2023 15:00:20

Number of reads: 6839974

Percentage reads mapped: 99.5

Strain: lineage4.5

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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00), embB p.Gly406Ala (0.99)
Pyrazinamide R pncA p.His71Arg (0.99)
Streptomycin R gid c.102delG (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (0.96)
Moxifloxacin R gyrA p.Asp94Gly (0.96)
Ofloxacin R gyrA p.Asp94Gly (0.96)
Levofloxacin R gyrA p.Asp94Gly (0.96)
Ciprofloxacin R gyrA p.Asp94Gly (0.96)
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
lineage4.5 Euro-American H;T RD122 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 7582 p.Asp94Gly missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Arg missense_variant 0.99 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.99 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 764061 p.Pro231Leu missense_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245118 p.Asn629Ser missense_variant 0.99
ethA 4327065 p.Cys137Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0