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

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.本数据集隶属于发表论文《等位变异赋予拟南芥适应小型区域环境差异》。下文将对每个文件进行简要说明。变异识别格式（Variant Call Format, VCF）文件中的样本命名规则遵循美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）生物样本（BioSample）数据库中的存储方式。各文件的具体生成流程详见论文正文。 Dartmap_Dutch_1001G_nuclear.vcf.gz：该文件基于拟南芥Col-0核基因组参考序列，在DartMap群体与荷兰1001G种质资源中鉴定得到变异集合，共包含2,712,612个双等位单核苷酸多态性（single nucleotide polymorphism, SNP）位点与353,974个双等位小型插入缺失（insertion-deletion, indel）位点，相关群体简称为DartMap + 1001G联合群体。 Dartmap_Dutch_1001G_mitochondrial.vcf.gz：该文件基于拟南芥Col-0线粒体基因组参考序列，在DartMap群体与荷兰1001G种质资源中鉴定得到变异集合，共包含231个双等位SNP位点与23个双等位小型indel位点，相关群体简称为DartMap + 1001G联合群体。 Dartmap_Dutch_1001G_chloroplast.vcf.gz：该文件基于拟南芥Col-0叶绿体基因组参考序列，在DartMap群体与荷兰1001G种质资源中鉴定得到变异集合，共包含400个双等位SNP位点与79个双等位小型indel位点，相关群体简称为DartMap + 1001G联合群体。 Dartmap_CNVs.vcf.gz：该文件包含在DartMap群体中基于拟南芥Col-0参考基因组鉴定得到的29,155个拷贝数变异（copy number variant, CNV）。 Dartmap_Dutch_1001G_neighbouring_countries_nuclear.vcf.gz：该文件为经过过滤的VCF文件，包含DartMap + 1001G联合群体及其周边国家种质的变异信息，基于拟南芥Col-0核基因组参考序列构建，用于论文中的群体结构分析。 Dartmap_Dutch_1001G_neighbouring_countries_mitochondrial.vcf.gz：该文件为经过过滤的VCF文件，包含DartMap + 1001G联合群体及其周边国家种质的变异信息，基于拟南芥Col-0线粒体基因组参考序列构建，用于论文中的群体结构分析。 Dartmap_Dutch_1001G_neighbouring_countries_chloroplast.vcf.gz：该文件为经过过滤的VCF文件，包含DartMap + 1001G联合群体及其周边国家种质的变异信息，基于拟南芥Col-0叶绿体基因组参考序列构建，用于论文中的群体结构分析。 Dartmap_GWAS_GEA.vcf.gz：该文件为经过过滤的VCF文件，包含DartMap群体中所有用于全基因组关联（genome-wide association, GWA）分析与基因组-环境关联（genome-environment association, GEA）分析的变异位点。 DartMap_phenotypical_data.xlsx：该文件包含DartMap群体的全部相关表型数据。 Dartmap_sample_ids_NCBI_sample_names.csv：该表格展示了每个DartMap样本的数字编号与对应NCBI BioSample ID的映射关系。