The new ARS-UCD1.2 assembly of the bovine genome has considerable improvements over the previous assembly and thus more accurate identification of patterns of genetic variation can be achieved with it. We explored differences in genetic variation between autosomes, the X chromosome, and the Y chromosome. In particular, variant densities, annotations, lengths (only for InDels), nucleotide divergence, and Tajima's D statistics between chromosomes were considered. Whole-genome DNA sequences of 217 individuals representing different cattle breeds were examined. The analysis included the alignment to the new reference genome and variant identification. 23,655,295 SNPs and 3,758,781 InDels were detected. In contrast to autosomes, both sex chromosomes had negative values of Tajima's D and lower nucleotide divergence. That implies a correlation between nucleotide diversity and recombination rate, which is obviously reduced for sex chromosomes. Moreover, the accumulation of nonsynonymous mutations on the Y chromosome could be associated with loss of recombination. Also, the relatively lower effective population size for sex chromosomes leads to a lower expected density of variants.