General Information of GWAS
Summary Statistics

General GWAS Summary
Project: Genetic dissection of shoot regeneration from root explants in Arabidopsis (Lardon et al. 2020, Commun. Biol.) Experiment Type Genome-wide Association Study
Date Started:Dec. 11, 2018, 2:43 p.m.Date Finished:Dec. 11, 2018, 2:50 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: shoots 15d protocol a Selected Transformation:SQRT
Selected Algorithm: EMMAX Histogram:
Algorithm Details
Number of SNPs before Filtering: 6973565 Number of SNPs after Filtering:1746081
Number of Samples before Filtering: 130 Number of Samples after Filtering: 130
AIC Null-Model: 128.04 AICc Null-Model:128.52
BIC Null-Model: 142.37
Variance Explained by the Null Model: -6.0e-03


authorstitlepub yearjournalvolumepagesdoi
Fran├žois Vasseur et al.Adaptive diversification of growth allometry in the plantArabidopsis thaliana2018Proceedings of the National Academy of Sciences1153416-342110.1073/pnas.1709141115
Danelle K. Seymour et al.Genetic architecture of nonadditive inheritance inArabidopsis thalianahybrids2016Proceedings of the National Academy of Sciences113E7317-E732610.1073/pnas.1615268113
Robin Lardon et al.The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors2020Communications Biology3N-A10.1038/s42003-020-01274-9
Jun Cao et al.Whole-genome sequencing of multiple Arabidopsis thaliana populations2011Nature Genetics43956-96310.1038/ng.911
Hyun Kang et al.Variance component model to account for sample structure in genome-wide association studies2010Nature Genetics42348-35410.1038/ng.548
Quan Long et al.Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden2013Nat Genet45884-89010.1038/ng.2678
Matthew Horton et al.Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel2012Nature Genetics44212-21610.1038/ng.1042
Robert J. Schmitz et al.Patterns of population epigenomic diversity2013Nature495193-19810.1038/nature11968
Susanna Atwell et al.Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines2010Nature465627-63110.1038/nature08800
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