easyGWAS - Detailed experiment information

General Information of GWAS

General GWAS Summary

Project:	mature seed tocopherols GWAS	Experiment Type	Genome-wide Association Study
esayGWAS-ID:	3766cb0b-db08-46a0-8eda-d027e6c9bd56	Owner:	alberte2
Date Started:	March 22, 2018, 4:11 p.m.	Date Finished:	March 22, 2018, 7:01 p.m.

Selected Species and Dataset

Selected Species:	Arabidopsis thaliana
Selected Dataset:	1001 Genomes Data
Selected Gene Annotation Set:	Gene Annotations (TAIR10)

Selected SNPs, Encodings and Filters

Selected SNPs:	All SNPs selected	MAF Filter:	0.05
SNP encoding:	Additive	Selected Principle Components:	3

Selected Phenotype

Phenotype Name:	BLUP aT	Selected Transformation:	None
Selected Algorithm:	EMMAX	Histogram:

Algorithm Details

Number of SNPs before Filtering:	6973565	Number of SNPs after Filtering:	1802374
Number of Samples before Filtering:	814	Number of Samples after Filtering:	814
AIC Null-Model:	-794.39	AICc Null-Model:	-794.32
BIC Null-Model:	-770.88
Variance Explained by the Null Model:	0.19

Top 10 SNPs (Bonferroni Correction, 0.05)

Publications

authors	title	pub year	journal	volume	pages	doi
Matthew Horton et al.	Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel	2012	Nature Genetics	44	212-216	10.1038/ng.1042
Susanna Atwell et al.	Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines	2010	Nature	465	627-631	10.1038/nature08800
Hyun Kang et al.	Variance component model to account for sample structure in genome-wide association studies	2010	Nature Genetics	42	348-354	10.1038/ng.548
Jun Cao et al.	Whole-genome sequencing of multiple Arabidopsis thaliana populations	2011	Nature Genetics	43	956-963	10.1038/ng.911
Robert J. Schmitz et al.	Patterns of population epigenomic diversity	2013	Nature	495	193-198	10.1038/nature11968
Quan Long et al.	Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden	2013	Nat Genet	45	884-890	10.1038/ng.2678
The 1001 Genomes Consortium et al.	1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana	2016	Cell	NA	N-A	10.1016/j.cell.2016.05.063
Danelle K. Seymour et al.	Genetic architecture of nonadditive inheritance inArabidopsis thalianahybrids	2016	Proceedings of the National Academy of Sciences	113	E7317-E7326	10.1073/pnas.1615268113
Elise Albert et al.	Genome-wide association identifies a missing hydrolase for tocopherol synthesis in plants	2022	Proceedings of the National Academy of Sciences	119	N-A	10.1073/pnas.2113488119