1001 Genomes Project: Whole genome sequencing data for the Eilenburg, Loch Ness and Slavice accessions of Arabidopsis thaliana Whole genome sequencing data for the Eilenburg, Loch Ness and Slavice accessions of the species Arabidopsis thaliana was generated as a part of the 1001 Genomes Project in order to create a complete catalog of genomic variations for these plants. We identified large deleted regions by intersecting data from short reads with tiling arrays with high true positive rate, base on validations by PCR amplification. Individual deletions were frequently observed in two or more of the accessions examined in this study. Arabidopsis thaliana 1001 genomes project bioproject 30811 PRJNA30811 true ENA-SAMPLE SRS006283-SRS006285 ENA-TAXID 3702 ENA-EXPERIMENT SRX011866-SRX011868,SRX030198,SRX030478-SRX030479,SRX031270 ENA-RUN SRR029163,SRR029315-SRR029316,SRR029469,SRR029569-SRR029571,SRR029573-SRR029575,SRR070311,SRR071243,SRR071410-SRR071411,SRR071794-SRR071796,SRR071958-SRR071960,SRR073127 ENA-SUBMISSION SRA009330 ENA-FASTQ-FILES http://www.ebi.ac.uk/ena/data/view/reports/sra/fastq_files/SRP001272 ENA-SUBMITTED-FILES http://www.ebi.ac.uk/ena/data/view/reports/sra/submitted_files/SRP001272 ENA-SPOT-COUNT 254721862 ENA-BASE-COUNT 15300995280