TB-Profiler result

Run: ERR4800205

Summary

Run ID: ERR4800205

Sample name:

Date: 20-10-2023 04:10:28

Number of reads: 3268853

Percentage reads mapped: 98.9

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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.Ser450Leu (0.97)
Isoniazid R fabG1 c.-15C>T (0.97), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Leu (0.99)
Pyrazinamide R pncA p.Trp68* (0.99)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.97)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (1.00)
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 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289038 p.Trp68* stop_gained 0.99 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Leu missense_variant 0.99 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 8040 p.Gly247Ser missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
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
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.94
thyA 3073883 p.Gly197Ser missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408010 p.Val65Phe missense_variant 0.99
gid 4408156 p.Leu16Arg missense_variant 1.0