TB-Profiler result

Run: ERR2516703
Summary

Run ID: ERR2516703

Sample name:

Date: 19-10-2023 23:40:45

Number of reads: 4479739

Percentage reads mapped: 99.52

Strain: lineage4.1.1

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.Thr400Ala (1.00), rpoB p.Ser450Leu (1.00)
Isoniazid R katG p.Tyr155Ser (0.97), ahpC c.-81C>T (1.00)
Ethambutol R embA c.-12C>T (0.99), embB p.Met306Leu (0.99)
Pyrazinamide R pncA p.Gly108Arg (1.00)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.752dupG (1.00), ethA c.752dupG (1.00)
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
lineage4.1 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 761004 p.Thr400Ala missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155648 p.Tyr155Ser missense_variant 0.97 isoniazid
pncA 2288920 p.Gly108Arg missense_variant 1.0 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 0.99 ethambutol
embB 4247429 p.Met306Leu missense_variant 0.99 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, ethionamide
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
mshA 576475 c.1129dupC frameshift_variant 1.0
rpoC 765150 p.Gly594Glu 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
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
katG 2155610 p.Ala168Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067514 p.Ser144Arg missense_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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0