Fig. 1
Flow chart of steps used to select SNPs for the Axiom genotyping array. SNPs on the Axiom array were selected from the Oregon State University (OSU) dataset described by Howe et al. [17] and the University of Hohenheim (UH) dataset described by Müller et al. [32]. ‘Discovered SNPs’ are the starting SNPs and isotigs from each dataset. Isotigs are transcript variants assembled using the Newbler de novo assembler. ‘Novel SNPs’ are SNPs in novel UH transcripts, which are transcripts missing from the OSU transcriptome [17]. ‘High-confidence SNPs’ are OSU SNPs with a target SNP probability (PS) < 0.001 or UH SNPs detected by 2 or 3 SNP detection programs. ‘Infinium genotyped SNPs’ are OSU SNPs previously genotyped using an Infinium genotyping array [17]. ‘Evaluated SNPs’ are the SNPs evaluated for suitability of flanking sequences. ‘Buildable SNPs’ are SNPs with at least one 35-nt flanking sequence with no other (i.e., non-target) high-confidence SNPs or indels. ‘Total buildable SNPs’ are the combined OSU and UH SNPs that were ranked for inclusion on the Axiom array using the variables described in Table 2