Table 5. Cross-classification of genotype calls for evaluating the protocols started from 5 ml of peripheral blood.

Compared sample		Peripheral blood from sample group #7 (All SNPs)					Concordance (%)	Kappa**
		AA	AB	BB	No call	Total
Peripheral blood from sample group #7 (as technical replicate)	AA	127,257	57	0	626	127,940
	AB	129	89,987	88	545	90,749
	BB	0	61	126,041	622	126,724
	No Call	936	509	859	895	3,199
	Total	128,322	90,614	126,988	2,688	348,612*	99.90	0.9985
LCL-hemolytic from sample group #7	AA	127,613	68	0	647	128,328
	AB	80	90,031	62	506	90,679
	BB	0	78	126,305	644	127,027
	No Call	629	437	621	891	2,578
	Total	128,322	90,614	126,988	2,688	348,612*	99.92	0.9987
LCL-gradient from sample group #7	AA	127,139	52	0	568	127,759
	AB	125	89,964	140	602	90,831
	BB	0	77	125,774	548	126,399
	No Call	1,058	521	1,074	970	3,623
	Total	128,322	90,614	126,988	2,688	348,612*	99.89	0.9983

^*Affy100k Array (116,204 SNPs) × 3 samples = 348,612 SNPs.

^**Closer to 1.0 indicates higher reproducibility.