General Information of GWAS
Summary Statistics

General GWAS Summary
Project: easyGWAS Paper (Case Study in A. thaliana) Experiment Type Genome-wide Association Study
esayGWAS-ID:57a7cf18-cb0f-408a-8954-49f94d1bfc47Owner: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

Publications


authorstitlepub yearjournalvolumepagesdoi
Matthew Horton et al.Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel2012Nature Genetics44212-21610.1038/ng.1042
Susanna Atwell et al.Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines2010Nature465627-63110.1038/nature08800
Christoph Lippert et al.FaST linear mixed models for genome-wide association studies2011Nature Methods8833-83510.1038/nmeth.1681
Jun Cao et al.Whole-genome sequencing of multiple Arabidopsis thaliana populations2011Nature Genetics43956-96310.1038/ng.911
Robert J. Schmitz et al.Patterns of population epigenomic diversity2013Nature495193-19810.1038/nature11968
Quan Long et al.Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden2013Nat Genet45884-89010.1038/ng.2678
The 1001 Genomes Consortium et al.1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana2016CellNAN-A10.1016/j.cell.2016.05.063