Table 3. Diversity statistics, by subspecies.

		No. of SNPs segregating				Avg. frequency of SNPs, %		Nucleotide level		Amino acid level
Subspecies	n	Total	Synonymous	Noncoding	Non-synonymous	Synonymous and noncoding	Non-synonymous	No. of alleles	% heterozygosity	No. of alleles	% heterozygosity
B. taurus	26	5	1	3	1	23.6	19.2	6	76.9	2	30.8
taurus
B. taurus	13	29	21	3	5	20.4	12.3	15	100.0	6	46.2
indicus

One Longhorn individual was found to have one typical taurine haplotype and one haplotype more typical of indicine cattle (14 SNPs removed from the most similar taurine haplotype). This may have resulted from a “breeding up” strategy that incorporated some B. taurus indicus genetic material in the background of this otherwise taurine individual. To avoid misrepresentation of taurine diversity, this individual was omitted from diversity and evolutionary inference statistics, although its haplotypes and SNPs are reflected elsewhere in this work.