With the incomplete genealogy, ϕest gave more precise estimates for related pairs, but ϕped and ϕpost characterized unrelated pairs better because of the intrinsic overestimation of kinship coefficients in this case (Figure 5). Because MLEs of the kinship coefficient of UN pairs were overestimated, this approach may not distinguish unrelated people from people sharing a common genetic background. On the other hand, based on only the part of the pedigree information used in the analysis, ϕped and ϕpost were 0 for some of the pairs that shared their unknown genetic background. This leads to an under-correction of relatedness and an inflated false positive rate. For related pairs, the mean squared error (MSE) of ϕest, ϕped and ϕpost was 1.1 ×10−4, 3.3 × 10−4 and 3.2 × 10−4 respectively. For unrelated pairs, the MSE of ϕest was 1.36 × 10−4 and the MSEs of ϕped and ϕpost were 0.
