easyGWAS - Detailed experiment information

General Information of GWAS

General GWAS Summary

Project:	easyGWAS Paper (Case Study in A. thaliana)	Experiment Type	Genome-wide Association Study
esayGWAS-ID:	57a7cf18-cb0f-408a-8954-49f94d1bfc47	Owner:	dgrimm
Date Started:	Oct. 9, 2016, 10:02 p.m.	Date Finished:	Oct. 10, 2016, 12:41 a.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:	0

Selected Phenotype

Phenotype Name:	RL	Selected Transformation:	BoxCox
Selected Algorithm:	FaSTLMM	Histogram:

Algorithm Details

Number of SNPs before Filtering:	6973565	Number of SNPs after Filtering:	1797912
Number of Samples before Filtering:	850	Number of Samples after Filtering:	850
AIC Null-Model:	4542.71	AICc Null-Model:	4542.71
BIC Null-Model:	4547.45
Variance Explained by the Null Model:	0.55

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
Christoph Lippert et al.	FaST linear mixed models for genome-wide association studies	2011	Nature Methods	8	833-835	10.1038/nmeth.1681
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