Table 2.

Summary of Estimated Contamination Levels $\hat{\mathit{\alpha }}$ Ratio of the Numbers of Heterozygous to Nonreference Allele Homozygous Genotypes, and Genotype Discordance with Array Data for 299 Samples from Type 2 Diabetes Study Using Sequence Data Only

Array Genotypes?	Measure	$\hat{\mathit{\alpha }}$(sequence only)
		<1%	1%–2%	2%–5%	≥5%
Yes (n = 227)	Number of samples	208	13	1	5
	− Before August 2010	81	13	1	5
	− After August 2010	127	0	0	0
	RR discordancea	0.0021	0.0030	0.0071	0.0492
	RA discordanceb	0.0154	0.0157	0.0172	0.0300
	AA discordancec	0.0085	0.0143	0.0377	0.176
	HET/HOM ratiod	1.92	1.84	2.16	2.66
No (n = 72)	Number of samples	46	8	7	11
	− Before August 2010	24	8	7	11
	− After August 2010	22	0	0	0
	HET/HOM ratiod	1.87	1.88	1.88	2.64

^aRR discordance: Genotype discordance when array-based genotype is homozygous reference

^bRA discordance: Genotype discordance when array-based genotype is heterozygous

^cAA discordance: Genotype discordance when array-based genotype in homozygous nonreference

^dHET/HOM ratio: Ratio of number of heterozygous genotypes to homozygous nonreference genotypes