TABLE 3.

Constitutional CNVs

	Detection method:	SNP array		Mate pair
	Detected by other method:	Yes	No	Yes	No	<5 probes
A	Gains	4	98	4	22	22
B	Losses	326	120	322	382	685
C	Total events	330	218	326	404	707
D	False-negative calls	—	1 (0.5%)	—	27 (7%)	—
E	Matches known CNV	326 (99%)	202 (93%)	319 (98%)	376 (93%)	92 (13%)
F	Median size (kb)	1.8	1.9	3.1	2.6	2.6
G	Median fold probe density vs. array	20.8	18.4	12.2	12.7	0.0
H	Median (log2R)	0.48	0.33	0.45	0.13	—
I	Median (Z statistic)	13.4	8.9	13.1	3.0	—
J	Median mate pairs	—	—	13	9	8
K	Median fraction mismatched bases	—	—	0.007	0.008	0.008
L	Created by inversion	1 (0.3%)	?	1 (0.3%)	3 (0.7%)	66 (9%)
M	Tandem repeat (losses only)	112 (34%)	82 (68%)	170 (53%)	291 (76%)	458 (67%)

?, cannot be determined; —, not applicable.