Table 1. Classes of primate segmental duplication.

				Copy-Number Corrected Duplicated Basepairs
Category	SD	SD >20 kbp	%Validation	HSA	PTR	PPY	MMU
HSA	51,458,805	15,236,422	89-92%	17,847,869
PTR	11,239,390	4,789,874	99%		16,583,946
PPY	30,553,228	6,417,679	98%			23,327,737
MMU	24,962,092	5,360,646	45%				45,810,964
MMU*	35,493,466	7,715,410	85%				18,266,656
HSA / PTR	32,392,480	21,061,194	NA	21,524,417	26,304,286
HSA / PTR / PPY	25,450,827	13,402,545	NA	11,259,061	14,012,351	11,541,148
HSA / PTR / PPY / MMU	14,094,156	7,156,616	NA	8,092,997	12,820,607	6,176,876	12,542,691
Total	190,150,978	73,424,976		58,724,344	69,721,190	41,045,761	30,809,347

Duplications were divided into eight categories based on the WSSD analysis of each primate genome (subsequent analysis were restricted to SDs >20 kbp in length). Lineage specific and shared duplication content are indicated. % validation indicates the fraction of species-specific duplications confirmed by cross-species array comparative genomic hybridization. Because the human genome was used, we corrected for copy number and examined sequence contigs not aligned to the human genome (see Methods). SDs assigned to the Y chromosome were not considered.

^*Macaque SDs detected in the macaque reference genome using WSSD and WGAC (<94% ID) approaches.