Associated dataset of Malus baccata 'Jackii' genome sequence

This dataset contains SNP sequence data generated from 184 F1 individuals derived from the cross 'Idared' × Malus baccata 'Jackii', as well as from both parental genotypes, produced for a genome analysis project. Genotyping was performed using tGBS® Genotyping-by-Sequencing with the restriction enzyme Bsp1286I, followed by sequencing on an Illumina HiSeq X platform. After debarcoding and trimming, the reads were aligned to the Malus baccata 'Jackii' reference genome (haplotype 1 and haplotype 2), and SNPs were called using only uniquely aligned reads. For each haplotype, a high-quality SNP dataset was generated, consisting of sites genotyped in at least 50% of the samples. The dataset includes the SNP context sequences for each haplotype (Apple.Chr.HT1/2.Analysis.MCR50.snps.ContextSequence201bp) as well as the corresponding tGBS genotyping data (Apple.Chr.HT1/2.Analysis.MCR50.snps.genotype). The dataset additionally contains the adjusted sequence (Mbj_HT1/Mbj_HT2.fasta), annotation data (final tandem repeat, TE final, EVM.final.gene, domain, motif, HT1 & HT2 new integrated functional annotation) and gene/peptides (cds.fasta, pep.fasta) sequence information.