Table 1. Repeats enriched and depleted in CNV breakpoints. The GC content and number of breakpoints are listed for the six CNV types.

CNV type	%GC	Breakpoints	Tandem repeats	G-quads	Alus
Terminal deletion	50.1	48	122	99**	62
Inverted duplication with terminal deletion	43.6	41	70	39*	36*
Translocation	46.1	21	40	24	42
Interstitial deletion	50.0	20	60	30	72**
Interstitial duplication	45.4	8	25	9	28**
Terminal duplication	41.0	2	1	0	2
Total		140	318	201	242

The number of tandem repeats, G-quadruplexes, and Alus per type of CNV are shown. Significant depletion (*) and enrichment (**) for repeats were determined by binomial test p-values <.00278 (.05/18, based on Bonferroni adjustment for 18 tests).