Fig. 4

Closer proximity between secondary polymorphisms and target SNPs result in decreased SNP inclusion and compatibility rates. Secondary polymorphisms and their positions were identified via sequence alignment of 53 cultivars to the GDDH13v1.1 genome. SNPs with accurate Infinium data were classified as included and SNPs with accurate Axiom data were deemed compatible (with Infinium data). The inclusion rate of Infinium data is represented by black. The compatibility of these included SNPs with Axiom data with and without class C SNPs (those with additional heterozygous cluster(s) in Axiom cluster plots requiring manual adjustment to make compatible) being classified as compatible are represented by pink and blue, respectively. The horizontal lines represent the inclusion and compatibility rates for SNPs with no identified secondary polymorphisms at their probe site for the three respective data sources that sized 6632 (black), 6011 (pink), and 6011 (blue) SNPs. SNPs included in this analysis had their alternate allele present in at least 10% of the sequenced individuals, had no more than 25% missing data across the sequenced individuals, and had probe sequence with a single BLAST hit on the GDDH13 WGS with an E-value <1E-12