The 1001 Genomes Consortium conducted a comprehensive study to reveal the global pattern of polymorphism in *Arabidopsis thaliana* using 1,135 accessions. The study involved two main pipelines, GMI-GATK and MPI-SHORE, for variant calling, which were validated in pilot studies. The pipelines were used to map reads to the *A. thaliana* TAIR10 reference genome, call SNPs and indels, and generate variant calls. The quality control and validation steps ensured that only high-quality accessions were included in the final dataset, resulting in 1,135 accessions. The study also included population genetic analyses, genome-wide association studies (GWAS), and the release of various data files and tools for further analysis. The data and tools are available on the 1001genomes project website.The 1001 Genomes Consortium conducted a comprehensive study to reveal the global pattern of polymorphism in *Arabidopsis thaliana* using 1,135 accessions. The study involved two main pipelines, GMI-GATK and MPI-SHORE, for variant calling, which were validated in pilot studies. The pipelines were used to map reads to the *A. thaliana* TAIR10 reference genome, call SNPs and indels, and generate variant calls. The quality control and validation steps ensured that only high-quality accessions were included in the final dataset, resulting in 1,135 accessions. The study also included population genetic analyses, genome-wide association studies (GWAS), and the release of various data files and tools for further analysis. The data and tools are available on the 1001genomes project website.