Table 1-1.

Mean overlap quantities (± SEM) in the dental caries dataset.

	HumanHap550	HumanHap610
	GC*	GC	non-GC	GC+filtering**
Num of duplicate samples (avg. CNV/sample)***	182 (18.6)	182 (79.4)	182 (61.1)	162 (54.1)
Num of non-duplicate samples(avg. CNV/sample)	1736 (26.6)	1736 (68.5)	1736 (92.9)	1512 (54.9)
Duplicate concordance rate	0.55(±0.02)	0.45(±0.02)	0.43(±0.02)	0.48(±0.02)
Unrelated pair concordance rate****	0.05(±0.003)	0.13(±0.004)	0.11(±0.004)	0.14(±0.004)
Father-child transmission rate	0.28(±0.006)	0.28(±0.005)	0.27(±0.005)	0.31(±0.005)
Mother-child transmission rate	0.28(±0.006)	0.27(±0.005)	0.26(±0.005)	0.31(±0.005)
Child inheritance rate	0.42(±0.009)	0.40(±0.008)	0.36(±0.008)	0.45(±0.008)

All mean overlap quantities were calculated as the average over pairs.

^*GC model adjustment procedure in PennCNV.

^**Samples were filtered by the criterion: LRR standard deviation (sd) > 0.3.

^***Number of duplicate samples (average number of CNVs per sample).

^****The unrelated pair concordance rate was calculated among father-mother pairs.