Different types of single nucleotide polymorphism (SNP) probes as clustered by GenomeStudio software in the HJ-DH population. (a) Distribution of the cluster separation score (CSS) for all 5306 SNPs; (b)-(f) Scoring of SNP genotyping data from different types of SNP probes. The three highlighted clusters denote the areas where the three different genotypes of homozygous allele AA (red), heterozygous AB (purple) and homozygous allele BB (blue) are called. Allele calls that are ambiguously located in the lighter colored areas between or below these areas are scored as “no call” (NC). Ellipses are used to mark the positions of the cluster calling areas. The dots with black circles are calls that needed to be manually re-checked and re-scored to missing data (“-”). (b) Typical score from probe bna1131 with two expected homozygous clusters (AA and BB); (c) The score from the SNP bna1686 with CSS <0.3 but with two clear parental genotype clusters; (d) The score from the SNP bna4154 with one parent being heterozygous (AB); (e) The score from the SNP bna4116 with one parent being NC; (f) The score from the SNP bna2547 with obvious 3 clusters (AA, AB, BB) in which the non-parental genotype of AB cannot be re-clustered to any homozygous cluster manually.