TB-Profiler result

Run: ERR2516532

Summary

Run ID: ERR2516532

Sample name:

Date: 19-10-2023 23:47:22

Number of reads: 2634944

Percentage reads mapped: 99.54

Strain: lineage4.1.1

Drug-resistance: MDR-TB


Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Ser (0.95)
Isoniazid R katG c.1571dupT (1.00), ahpC c.-48G>A (1.00), ahpC c.-39C>T (1.00)
Ethambutol R embB p.Asp354Ala (1.00), embB p.Gln497Pro (1.00)
Pyrazinamide R pncA c.-11A>G (1.00)
Streptomycin R rpsL p.Lys88Gln (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyA p.Phe152Val (0.90)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
rpoB 761139 p.His445Ser missense_variant 0.95 rifampicin
rpsL 781821 p.Lys88Gln missense_variant 1.0 streptomycin
katG 2154540 c.1571dupT frameshift_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
ahpC 2726154 c.-39C>T upstream_gene_variant 1.0 isoniazid
thyA 3074018 p.Phe152Val missense_variant 0.9 para-aminosalicylic_acid
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Pro 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
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrB 7221 p.Ser661Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766653 p.Ser1095Phe missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 1.0
embR 1417416 c.-69G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673865 c.-337C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C 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
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4327059 p.Gly139Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408275 c.-73G>C upstream_gene_variant 1.0