Table 3. Comparison of kinship estimation with and without off-target data in WES of 762 Chinese and Malays.

Dataset	Method	Unrelated (289,205 pairs)		3rd degree (148 pairs)		2nd degree (147pairs)		PO/FS (437 pairs)		Self-kinship (762 individuals)
		RMSE	BIAS	RMSE	BIAS	RMSE	BIAS	RMSE	BIAS	RMSE	BIAS
Target	SEEKIN	0.006	-0.001	0.007	-0.001	0.008	-0.003	0.010	-0.004	0.018	-0.005
	PC-Relate	0.005	0.000	0.007	-0.001	0.008	-0.004	0.012	-0.008	0.022	-0.017
Target + off-target	SEEKIN	0.003	-0.001	0.003	0.001	0.004	0.001	0.007	0.003	0.017	0.002
	PC-Relate	0.002	0.000	0.004	-0.004	0.009	-0.009	0.019	-0.019	0.026	-0.021

Evaluation was based on SNPs overlapped with the SGVP dataset in the BEAGLE+1KG3 call set of 762 individuals for both SEEKIN and PC-Relate. 40,824 SNPs within target regions and 1,054,229 SNPs across target and off-target regions were included in the analyses. RMSE is the root mean squared error and BIAS is defined as the mean difference to the array-based estimates from PC-Relate for each type of relatedness. Negative values of BIAS suggest underestimation for results based on sparse sequencing data and vice versa.