For each of three Danish dairy cattle breeds, Danish Holstein, Danish Red Dairy Cattle and Danish Jersey Cattle approximately 30 key ancestors were sequenced to a depth of about 10X. These key ancestors were chosen to maximize their contributions to present day populations. The three breeds are compared with respect to differences in amount of sequence variation observed. The observed patterns in and differences between breeds are interpreted in the light of known individual and population histories. Also, patterns of occurrence of short indels are compared. Particular attention is paid to variants that occur in several of the breeds. Regions occurring in multiple breeds and suspected of harboring lethal or sub lethal sequence variants are examined for similarities across breeds in occurrence of sequence variants.