Table 3. Distribution of orthologous score (OS) for macaques.

	OS = 0	OS = 1	OS = 2
Length	1.78 M	35.16 M	0.68 M
Percent of target region	4.73%	93.45%	1.82%

A fragment from the target region of the human reference genome was aligned to the Indian macaque reference genome. The OS was calculated for every site and classified into three possible levels: OS = 0, no alignment hit, unable to be captured theoretically; OS = 1, only one hit, high level of 1∶1 orthologous, well covered; OS = 2, multiple hits at different locations in the macaque reference, would give rise to misalignment and potentially false polymorphisms.