Table 2  Proportions of genome and of segments for the different ibd state types
ibd stateAll ibdThree ibdTwo pairsOne pairNo ibd
Percentage of genome
Simulated0.00420.200.1211.5888.10
Prior, β = 0.020.00450.300.1110.8788.72
Inferred: β = 0.02 Hap.0.02170.410.1512.6586.76
Gen.0.01890.270.1410.3089.27
Inferred: β = 0.05 Hap.0.03030.510.1913.7185.55
Gen.0.03040.320.1711.1788.31
Segment length (Mbp)
Simulated0.710.440.400.786.44
Inferred: β = 0.02 Hap.0.250.400.420.886.72
Gen.0.260.460.571.2111.49
Inferred: β = 0.05 Hap.0.270.360.380.785.57
Gen.0.290.420.491.099.57
Percentage of segments
Simulated0.021.551.0250.6946.73
Prior, β = 0.020.041.920.9650.8246.22
Inferred: β = 0.02 Hap.0.303.621.2750.0144.81
Gen.0.423.341.4549.5945.20
Inferred: β = 0.05. Hap.0.334.081.4550.2443.90
Gen0.513.701.7049.5044.58
  • 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.