Fig. 3

Genomic prediction bias, defined as \({\beta }_{1}-1\), where \({\beta }_{1}\) is the regression coefficient of the 35 k SNP array genomic estimated breeding values ~ Oxford Nanopore Technologies derived genomic estimated breeding values, for the four different imputation approaches across the sequencing coverages for four traits: body weight (BW), body condition score (BCS), corpus luteum score (CL score) and hip height (HH). Labels at the top of each figure indicate the imputation method used starting with GLIMPSE [22], minor allele count (MAC) genotyping with Beagle5.2 [18], quality score (Q-score) genotyping with Beagle5.2 and QUILT [21]. Prediction bias was also calculated across five different SNP reference panel sizes which were created using minor allele frequency (MAF) filters from whole genome sequence SNP. The smallest SNP reference panel, the bovine high definition (HD) SNP, had only the 641 k SNP used to calculate the GEBVs