Discovery of genomic variants associated with genebank historical traits for rice improvement: SNP and indel data, phenotypic data, and GWAS results

This dataset provides supporting information for Sanciangco et al (submitted) consisting of: A) file list, tables of phenotypes for quantitative and categorical traits and trait descriptions, and tables of SNP/indel numbers for Filtered, LD-pruned and subpopulation datasets (7 files named as "00_*"); B) plink files for Filtered and LD-pruned SNP/indel datasets for all genotypes and for indica, japonica and aus subsets (15 fIles named as "01_*"); C) EMMAX results on Filtered dataset for 12 quantitative traits on All, Aus, Indica, and Japonica genotypes and corresponding Manhattan and QQ plots (144 files named as "0[2345]_*"); D) EMMAX results on LD-pruned dataset for 12 quantitative traits on All, Aus, Indica, and Japonica genotypes and corresponding Manhattan and QQ plots (72 files named as "0[6789]_*"); E) EMMAX results on LD-pruned dataset for 20 categorical traits treated as numeric on All genotypes and corresponding Manhattan and Q-Q plots (60 files named as "10_*"); F) Anova results obtained on numerically transformed LD-pruned dataset for 20 categorical traits on All genotypes and corresponding Manhattan plots (40 files named as "11_*").