Table 2 . Proportions of genome and of segments for the different ibd state types.

ibd state	All ibd	Three ibd	Two pairs	One pair	No ibd
Percentage of genome
Simulated	0.0042	0.20	0.12	11.58	88.10
Prior, β = 0.02	0.0045	0.30	0.11	10.87	88.72
Inferred: β = 0.02 Hap.	0.0217	0.41	0.15	12.65	86.76
Gen.	0.0189	0.27	0.14	10.30	89.27
Inferred: β = 0.05 Hap.	0.0303	0.51	0.19	13.71	85.55
Gen.	0.0304	0.32	0.17	11.17	88.31
Segment length (Mbp)
Simulated	0.71	0.44	0.40	0.78	6.44
Inferred: β = 0.02 Hap.	0.25	0.40	0.42	0.88	6.72
Gen.	0.26	0.46	0.57	1.21	11.49
Inferred: β = 0.05 Hap.	0.27	0.36	0.38	0.78	5.57
Gen.	0.29	0.42	0.49	1.09	9.57
Percentage of segments
Simulated	0.02	1.55	1.02	50.69	46.73
Prior, β = 0.02	0.04	1.92	0.96	50.82	46.22
Inferred: β = 0.02 Hap.	0.30	3.62	1.27	50.01	44.81
Gen.	0.42	3.34	1.45	49.59	45.20
Inferred: β = 0.05. Hap.	0.33	4.08	1.45	50.24	43.90
Gen	0.51	3.70	1.70	49.50	44.58

Results are given both as for the simulated data, under the prior model for β = 0.02, and as inferred using ibd haplo using either haplotypic (Hap.) or genotypic (Gen.) data with γ = 0.1 and for β = 0.02 and β = 0.05 in the analysis (δ = 0.1). For clearer comparison with the simulation truth and model prior, the no-call sites have been excised from the ibd haplo output, and proportions and lengths computed using only the marker locations at which a call was made.