Additional file 1 of Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Additional file 1: Table S1. Name and details of 672 rice varieties. Detailing read number, mapping statistics, Vietnamese National Genebank number, local name, location, characteristic, subtype and subpopulation. Table S2. Name and details of 3635 rice varieties. Detailing the new subpopulation and PCO analysis. Table S3. Phenotypic measurements for 20 traits for 672 samples. Detailing individual measurements for each sample, description of phenotypes, statistics for all samples and individually for the Indica and Japonica subtypes. Phenotypes are available for around 75% of the samples. Table S4. Phenotype abbreviations and details. Table S5. Phenotype statistics (mean and coefficient of variation) and population comparisons (t-test). Table S6. Diversity (π) of each subpopulation. Table S7. GWAS results. List of the 21 QTL and the positions of the individual QTLs for each panel. Table S8. Gene lists for the 21 QTL. Table S9 List of 107 IRRI rice samples. Detailing IRRI accession, country on origin, K9 and K15 group and Vietnamese subpopulation. Table S10. List of 14 SNP sets used for analysis. Detailing filtering parameters, sample and SNP numbers for each SNP set. Table S11. Summary count of SNPs with effects on the genome. Detailing SnpEff annotation of the full set of 3,750,621 SNPs using the Oryza sativa MSU release 7 rice annotation. Six tables detailing number of effects by impact, functional class, type, region, base changes and Ts/Tv ratio.