TB-Profiler result

Run: ERR3287855
Summary

Run ID: ERR3287855

Sample name:

Date: 20-10-2023 05:51:44

Number of reads: 3483390

Percentage reads mapped: 99.66

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.Asp435Tyr (1.00)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Asp94Tyr (0.32)
Moxifloxacin R gyrA p.Asp94Tyr (0.32)
Ofloxacin R gyrA p.Asp94Tyr (0.32)
Levofloxacin R gyrA p.Asp94Tyr (0.32)
Ciprofloxacin R gyrA p.Asp94Tyr (0.32)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.311dupG (0.50), tlyA c.311dupG (0.50)
Kanamycin
Cycloserine
Ethionamide R ethA c.672_673dupGC (0.77), ethA c.672_673dupGC (0.77)
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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7581 p.Asp94Tyr missense_variant 0.32 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
tlyA 1918248 c.311dupG frameshift_variant 0.5 capreomycin, capreomycin
ethA 4326800 c.672_673dupGC frameshift_variant 0.77 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 6579 p.Ser447Tyr missense_variant 0.6
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
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
mmpL5 776216 c.2265G>T synonymous_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155295 p.Gly273Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726152 c.-41C>A upstream_gene_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.99
embC 4240137 p.Ala92Gly missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407844 p.Glu120Ala missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0