TB-Profiler result

Run: ERR040137

Summary

Run ID: ERR040137

Sample name:

Date: 20-10-2023 23:52:06

Number of reads: 14795000

Percentage reads mapped: 99.24

Strain: lineage4.1.1.3

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.His445Tyr (0.99)
Isoniazid R ahpC c.-81C>T (0.99), katG c.-653_388del (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Leu4Ser (0.99)
Streptomycin
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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.His445Tyr missense_variant 0.99 rifampicin
pncA 2289231 p.Leu4Ser missense_variant 0.99 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
katG 2155723 c.-653_388del frameshift_variant 1.0 isoniazid
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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776362 p.Gln707Lys missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673373 c.-66_-57delCAGCCACGTT upstream_gene_variant 1.0
rpsA 1834022 p.Leu161Val missense_variant 0.99
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 4248004 p.Gln497His missense_variant 0.98
embB 4249408 c.2895G>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407961 p.Ile81Thr missense_variant 0.97