Table 6. .

Sequence Properties of Variant and Invariant Regions^[Note]

		Average
Interval	No. of Regions	Length (kb)	Exon Density (Mb)	Duplication Depth (copies)	Alignment Length (kb)a	Identitya
Variant	84	2,923	103.4	2.4	54	.9819
Invariant	46	615	132.6	1.8	41	.9819

Note.— Of the 130 regions targeted by the segmental duplication array, those that have been associated with a CNP in both this study and our previous work³ were considered “variant”; those regions in which no CNPs were detected were labeled “invariant.” It should be emphasized that, in most cases, copy-number variation does not extend over the entire interval but is restricted to the segmental duplication embedded within the boundaries of the interval. The regions targeted by the segmental duplication array were selected using the criteria of flanking paired intrachromosomal segmental duplications >50 kb and <10 Mb apart, >10 kb in length, and >95% sequence identity, resulting in the identification of 1,124 intervals across the hg16 genome assembly. The 1,124 intervals, however, extensively overlapped because of the clustered nature of segmental duplications in the genome; thus, the 1,124 intervals were collapsed into 130 nonredundant regions.

^aAverage alignment length and identity were calculated on the basis of the total set of redundant intervals (n=1,124).