The study presents the first phase of the 1001 Genomes Project, which sequenced 80 Arabidopsis thaliana strains from eight geographic regions to identify genetic variation contributing to adaptation. The analysis revealed a large number of common SNPs and small indels, as well as larger structural variants (SVs), and their effects on gene function and population structure. The study also identified patterns of linkage and local and global genetic diversity. The results show that the effective population size of A. thaliana is between 250,000 and 300,000, and that recent selective sweeps are rare, while potentially deleterious mutations are more common in marginal populations. The study also compared the mutation spectrum of A. thaliana with that of its relative A. lyrata, revealing a bias towards G:C→A:T transitions in the greenhouse. The study also identified a large number of deleterious mutations, including premature stop codons and frameshifts, and found that many of these mutations are likely to be functional. The study also developed a web application for querying and analyzing polymorphism data. The results provide a comprehensive view of the genetic diversity of A. thaliana and will be useful for genome-wide association studies (GWAS) and for understanding the genetic basis of adaptation. The study also highlights the importance of population structure and genetic heterogeneity in GWAS, and suggests that improved sequencing methods will enable the complete reconstruction of alleles in the future.The study presents the first phase of the 1001 Genomes Project, which sequenced 80 Arabidopsis thaliana strains from eight geographic regions to identify genetic variation contributing to adaptation. The analysis revealed a large number of common SNPs and small indels, as well as larger structural variants (SVs), and their effects on gene function and population structure. The study also identified patterns of linkage and local and global genetic diversity. The results show that the effective population size of A. thaliana is between 250,000 and 300,000, and that recent selective sweeps are rare, while potentially deleterious mutations are more common in marginal populations. The study also compared the mutation spectrum of A. thaliana with that of its relative A. lyrata, revealing a bias towards G:C→A:T transitions in the greenhouse. The study also identified a large number of deleterious mutations, including premature stop codons and frameshifts, and found that many of these mutations are likely to be functional. The study also developed a web application for querying and analyzing polymorphism data. The results provide a comprehensive view of the genetic diversity of A. thaliana and will be useful for genome-wide association studies (GWAS) and for understanding the genetic basis of adaptation. The study also highlights the importance of population structure and genetic heterogeneity in GWAS, and suggests that improved sequencing methods will enable the complete reconstruction of alleles in the future.