Table 2.

Simulation results for offspring of first cousins (1C), second cousins (2C) and third cousins (3C).

			Correlation coefficients
		Mean [95% CI]	True HBD	FPLINK	FADC	FEstimSPT	FEstim
1C	True HBD	0.062 [0.019-0.121]	1.00	0.82	0.82	0.86	0.91
	FPLINK	0.063 [0.005-0.129]	0.82	1.00	1.00	0.95	0.78
	FADC	0.063 [0.006-0.129]	0.82	1.00	1.00	0.95	0.78
	FEstimSPT	0.063 [0.004-0.128]	0.86	0.95	0.95	1.00	0.82
	FEstim	0.063 [0.020-0.115]	0.91	0.78	0.78	0.82	1.00
2C	True HBD	0.015 [0.000-0.045]	1.00	0.51	0.51	0.56	0.87
	FPLINK	0.018 [0.000-0.059]	0.51	1.00	0.99	0.82	0.52
	FADC	0.018 [0.000-0.059]	0.51	0.99	1.00	0.83	0.52
	FEstimSPT	0.016 [0.000-0.055]	0.56	0.82	0.83	1.00	0.58
	FEstim	0.016 [0.000-0.045]	0.87	0.52	0.52	0.58	1.00
3C	True HBD	0.004 [0.000-0.020]	1.00	0.22	0.22	0.26	0.77
	FPLINK	0.009 [0.000-0.041]	0.22	1.00	0.97	0.70	0.25
	FADC	0.009 [0.000-0.040]	0.22	0.97	1.00	0.71	0.26
	FEstimSPT	0.007 [0.000-0.035]	0.26	0.70	0.71	1.00	0.30
	FEstim	0.004 [0.000-0.023]	0.77	0.25	0.26	0.30	1.00

All F_PLINK and F_ADC values that were negative were set to zero in these correlations, in order to allow comparisons across different methods since FEstim does not provide negative values.

Correlation coefficient is for comparing each method to the true proportion of markers that are homozygous by descent ("True HBD" line).