TB-Profiler result

Run: ERR4813796
Summary

Run ID: ERR4813796

Sample name:

Date: 20-10-2023 14:54:42

Number of reads: 2317266

Percentage reads mapped: 99.64

Strain: lineage4.3.2;lineage4.1.1.3

Drug-resistance: RR-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 (0.76)
Isoniazid
Ethambutol
Pyrazinamide
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.72
lineage4.1 Euro-American T;X;H None 0.31
lineage4.3.2 Euro-American (LAM) LAM3 None 0.73
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.3
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.31
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 761155 p.Ser450Leu missense_variant 0.76 rifampicin
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.68
rpoC 765150 p.Gly594Glu missense_variant 0.39
rpoC 766488 p.Pro1040Arg missense_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.68
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155683 p.Lys143Asn missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289017 c.225T>C synonymous_variant 0.28
kasA 2519131 c.1017G>T synonymous_variant 0.75
thyA 3073868 p.Thr202Ala missense_variant 0.69
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3986910 p.Arg23Trp missense_variant 0.68
clpC1 4038287 c.2418C>T synonymous_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.31
embB 4248914 p.Ala801Thr missense_variant 0.72
embB 4249408 c.2895G>A synonymous_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.6