Datasets belonging to the publication "Allelic variants confer Arabidopsis adaptation to small regional environmental differences". (Q6691439)

Datasets belonging to the publication "Allelic variants confer Arabidopsis adaptation to small regional environmental differences". A short description of each file is found below. Samples in the Variant Call Format (VCF) files are named according to how they are stored in the National Center for Biotechnology Information (NCBI) BioSample database. Detailed descriptions of how each file was generated are found in the manuscript. Dartmap_Dutch_1001G_nuclear.vcf.gz 2,712,612 bi-allelic SNPs and 353,974 bi-allelic small indels called in the DartMap panel and the Dutch 1001G accessions (collectively referred to as DartMap + 1001G panel for brevity) relative to the Arabidopsis thaliana Col-0 nuclear genome reference sequence. Dartmap_Dutch_1001G_mitochondrial.vcf.gz 231 bi-allelic SNPs and 23 bi-allelic small indels called in the DartMap panel and the Dutch 1001G accessions (collectively referred to as DartMap + 1001G panel for brevity) relative to the A. thaliana Col-0 mitochondrial genome reference sequence. Dartmap_Dutch_1001G_chloroplast.vcf.gz 400 bi-allelic SNPs and 79 bi-allelic small indels called in the DartMap panel and the Dutch 1001G accessions (collectively referred to as DartMap + 1001G panel for brevity) relative to the A. thaliana Col-0 chloroplast genome reference sequence. Dartmap_CNVs.vcf.gz 29,155 copy number variants (CNVs) called in the DartMap panel relative to the A. thaliana Col-0 reference genome. Dartmap_Dutch_1001G_neighbouring_countries_nuclear.vcf.gz Filtered VCF file containing variants of the DartMap + 1001G panel and that of neighbouring countries relative to the A. thaliana Col-0 nuclear genome reference sequence. Used for population structure analysis in the manuscript. Dartmap_Dutch_1001G_neighbouring_countries_mitochondrial.vcf.gz Filtered VCF file containing variants of the DartMap + 1001G panel and that of neighbouring countries relative to the A. thaliana Col-0 mitochondrial genome reference sequence. Used for population structure analysis in the manuscript. Dartmap_Dutch_1001G_neighbouring_countries_chloroplast.vcf.gz Filtered VCF file containing variants of the DartMap + 1001G panel and that of neighbouring countries relative to the A. thaliana Col-0 chloroplast genome reference sequence. Used for population structure analysis in the manuscript. Dartmap_GWAS_GEA.vcf.gz Filtered VCF file containing all variants of the DartMap panel that were used for all genome-wide association (GWA) and genome-environment association (GEA) analyses. DartMap_phenotypical_data.xlsx All relevant phenotypical data of the DartMap panel. Dartmap_sample_ids_NCBI_sample_names.csv Table showing which numerical ID of each DartMap sample corresponds to which NCBI BioSample ID.