VCF file of 1163 ecotypes of Arabidopsis thaliana supporting Brachi et al. (2022)

This is a VCF file containing 7 million SNP genotype calls for 1163 ecotypes of Arabidopsis thaliana, supporting the following manuscript: Brachi, Benjamin, et al. "Plant genetic effects on microbial hubs impact host fitness in repeated field trials." Proceedings of the National Academy of Sciences 119.30 (2022): e2201285119. This extends previous work by the Arabidopsis Genome Consortium (2016) who generated short-read illumina data for 1135 ecotypes, and used them to call SNP genotypes using bcftools. Brachi et al added an additional 28 ecotypes, and repeated the SNP calls using GATK best practices. These additional short read data can be found on the European Nucleotide Archive, project PRJEB123400. Please note that it is likely that ecotypes Röd-17-319 and Bil-3 (1435 and 5835) are likely to be incorrect. The metadata for these lines indicates that they should be from the Swedish High Coast, but the genotypes cluster with other ecotypes from Alestenar in southern Sweden. They are included here for completeness.