Figure 5

Sorted pairwise numbers of opposing homozygotes with ohplot. The plot is useful to guide decisions for parameter settings to reconstruct the pedigree. The separation value is the maximum separation found between sorted value pairs divided by the maximum number of opposing homozygotes. The cut off value is the number of SNP at the mid-point of the largest separation (red line). The other lines are the average number of opposing homozygotes expected in full-sib families (cyan – not shown here), half-sib families (green) and in unrelated individuals (blue) according to [12]; plus the 90% threshold used for pedigree reconstruction (pink). The function can also be used with pedigree information to detect inconsistencies (relations are colour coded according to the pedigree to facilitate visualization). The plot is from 106 Hanwoo cattle from 14 family groups genotyped on the 700 k Illumina BeadChip array.