TB-Profiler result

Run: ERR1679638
Summary

Run ID: ERR1679638

Sample name:

Date: 19-10-2023 11:52:55

Number of reads: 1008454

Percentage reads mapped: 99.78

Strain: lineage4.6.5

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), rpoC p.Phe452Ser (1.00)
Isoniazid
Ethambutol R embA c.-12C>T (1.00), embB p.Met306Ile (1.00), embB p.Ala313Val (1.00)
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Asp94His (1.00)
Moxifloxacin R gyrA p.Asp94His (1.00)
Ofloxacin R gyrA p.Asp94His (1.00)
Levofloxacin R gyrA p.Asp94His (1.00)
Ciprofloxacin R gyrA p.Asp94His (1.00)
Aminoglycosides
Amikacin
Capreomycin R tlyA p.Asn236Lys (1.00)
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
lineage4.6.5 Euro-American T;LAM None 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 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764724 p.Phe452Ser missense_variant 1.0 rifampicin
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247451 p.Ala313Val 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_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 2155667 p.Trp149Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288806 p.Ala146Pro missense_variant 1.0
folC 2746995 p.Val202Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
gid 4407908 c.294delC frameshift_variant 1.0
PPE35 2170007 c.544_605delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG frameshift_variant 1.0