easyGWAS - Detailed experiment information

General Information of GWAS

General GWAS Summary

Project:	Genome-wide association study of 107 phenotypes (Atwell et al.)	Experiment Type	Genome-wide Association Study
esayGWAS-ID:	5df10ad3-7361-4d07-b86d-eaa107d8cf81	Owner:	dgrimm
Date Started:	Sept. 30, 2014, 11:58 a.m.	Date Finished:	Sept. 30, 2014, noon

Selected Species and Dataset

Selected Species:	Arabidopsis thaliana
Selected Dataset:	AtPolyDB (call method 75, Horton et al.)
Selected Gene Annotation Set:	Gene Annotations (TAIR9)

Selected SNPs, Encodings and Filters

Selected SNPs:	All SNPs selected	MAF Filter:	0.1
SNP encoding:	Additive	Selected Principle Components:	0

Selected Phenotype

Phenotype Name:	Germ 22	Selected Transformation:	None
Selected Algorithm:	EMMAX	Histogram:

Algorithm Details

Number of SNPs before Filtering:	214051	Number of SNPs after Filtering:	175373
Number of Samples before Filtering:	177	Number of Samples after Filtering:	177
AIC Null-Model:	276.31	AICc Null-Model:	276.33
BIC Null-Model:	279.48
Variance Explained by the Null Model:	-4.5e-02

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
Jun Cao et al.	Whole-genome sequencing of multiple Arabidopsis thaliana populations	2011	Nature Genetics	43	956-963	10.1038/ng.911
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