Fig. 2

Correlations between body weight (BW) genomic estimated breeding values (GEBV) derived from 35 k SNP array genotypes and BW GEBVs derived from Oxford Nanopore Technologies (ONT) data. ONT GEBVs were imputed using four different imputation strategies and across five sequencing coverages. Labels at the top of the figure indicate the imputation method used starting from left to right with GLIMPSE [22], minor allele count (MAC) genotyping with Beagle5.2 [18], quality score (Q-score) genotyping with Beagle5.2 and QUILT [21]. SNP reference panel size is indicated by the minor allele frequency (MAF) filter on the right-hand side in descending order of size from top to bottom. The largest panel had 48,203,338 SNP and was referred to as the No MAF filter panel, while the smallest panel was referred to as the bovine high density (HD) SNP which had only the 641 k SNP used to calculate the GEBVs. Error bars indicate 95% confidence of the Pearson correlation