Single nucleotide polymorphism in hapmap format for GWAS analysis using Arabidopsis thaliana MAGIC lines

GZ compressed tsv file in hapmap format with all binary SNPs for which data is available in at least 50% of the MAGIC lines sequenced. Used in Ricachenevsky et al 2025, Comparison of linkage and association mapping in MAGIC lines identifies AtMTP3 as a new gene controlling natural variation in leaf zinc concentration in Arabidopsis J. Exp. Botany This data set follows from the following work Magic lines creation: Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5: e1000551. doi: 10.1371/journal.pgen.1000551. Magic lines sequenced and imputed: Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R (2017) Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics 205: 1425-1441. doi: 10.1534/genetics.116.192823