Additional file 1: Figure S1. Comparison of the results of cLDLA mapping with the results of case–control homozygosity mapping. The blue line with blue dots represents the results of the cLDLA mapping approach using data on 43 Weaver-affected, 31 Weaver carriers and 86 Weaver-free animals which resulted in a maximum LRT value (LRT = 73.9) at position 49,812,384 bp. The corresponding 0.853-Mb confidence interval between SNPs at 49,514,652 and 50,367,484 bp, represented by the grey bar, is assumed to harbor the causative mutation. The black line with black squares represents the results of a case–control homozygosity mapping approach [37] based on all Weaver-affected (case group) and Weaver-free animals (control group) from the cLDLA mapping population. In a second run, all Weaver cases which had been identified as phenocopies in the course of our further analyses were removed from the case group. The results of this run are displayed by the red line with red squares. Only run 2 of the homozygosity mapping approach, i.e. after removal of the phenocopies which were identified later, displayed a significant association with a 1.913-Mb block of adjacent SNPs (between 48,408,626 and 50,412,884 bp). However, the cLDLA approach was able to map the Weaver locus to the same chromosomal region even if the phenocopies were still included in the mapping population. Furthermore, the 0.853-Mb confidence interval identified by the cLDLA method allows for more precise analyses than the 1.913-Mb block of SNPs identified by homozygosity mapping, accounting for the higher mapping resolution obtained by the cLDLA method.