Fig. 4
From: Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Manhattan plots for fat percentage, protein percentage, and milk yield. Number of significantly (P < 10-8) associated variants in GWAS for seven traits. Estimated genomic heritability for stature and six dairy traits. Manhattan plots showing association of sequence variants - imputed using ARS-UCD1.2 (blue and grey) and UOA_Angus_1 (orange and grey) - with fat percentage (a), protein percentage (b) and milk yield (c). The orientation of some autosomes (e.g., chromosome 14 & chromosome 20) is flipped between ARS-UCD1.2 and UOA_Angus_1. The number (in thousands) of variants - imputed using ARS-UCD1.2 (blue) and UOA_Angus_1 (orange) - significantly (P < 10-8) associated with the seven traits considered for GWAS (d). Genomic heritability estimated using all autosomal variants imputed using ARS-UCD1.2 (blue) and UOA_Angus_1 assemblies (orange) (e). Standard errors of the estimates are indicated in read lines