Table 4  The ibd segment inference at decreasing levels of smoothing
α:0.010.050.10.52.0
% by mrk:Hap.Gen.Hap.Gen.Hap.Gen.Hap.Gen.Hap.Gen.
A. Given ibd (12%)
Correct75.656.874.757.873.556.964.945.648.324.9
Other ibd1.71.52.32.02.72.54.33.86.14.5
False neg.9.420.95.613.34.010.31.54.70.52.6
No call13.320.817.426.919.830.329.345.945.268.0
B. Given no ibd (88%)
Correct90.089.780.481.074.175.252.655.929.334.3
False pos.2.22.33.83.44.73.96.64.46.43.2
No call7.88.015.715.621.220.940.739.764.362.5
  • Results are shown at decreasing levels of smoothing, that is, increasing prior change-rate parameter α, and are tabulated as percentages over the 6913 markers over all 500 pairs of individuals. They are given for analyzing the data on the 500 pairs both as four haplotypes (Hap.) and as pairs of genotypes (Gen.). Results are separated into (A) the 12% of genome in which the latent ibd-state involves some ibd and (B) the 88% of genome in the no-ibd state.