Table 2.
Kinship-Coefficient Estimates for Population-Structure Setting 2 with REAP, KING-Robust, and the Homogeneous-Population Estimator
| Outbred Relationship |
ϕ (Kinship Coefficient) |
|||
|---|---|---|---|---|
| Theoretical Kinship Coefficient | REAP Estimate (SD) | Homogeneous Estimate (SD) | KING-Robust Estimate (SD) | |
| Parent-offspring pair | 0.25 | 0.251 (0.008) | 0.291 (0.014) | 0.249 (0.005) |
| Full siblings | 0.25 | 0.251 (0.007) | 0.291 (0.016) | 0.251 (0.005) |
| Second degree | 0.125 | 0.126 (0.006) | 0.172 (0.016) | 0.125 (0.007) |
| Third degree | 0.0625 | 0.063 (0.005) | 0.113 (0.016) | 0.062 (0.008) |
| Fourth degree | 0.03125 | 0.031 (0.005) | 0.084 (0.014) | 0.033 (0.008) |
| Unrelated: similar ancestry | 0 | −0.0001 (0.005) | 0.054 (0.017) | −0.002 (0.010) |
| Unrelated: different ancestry | 0 | −0.0001 (0.005) | −0.055 (0.017) | −0.135 (0.040) |
Kinship coefficients were estimated with the REAP kinship-coefficient estimator from Equation 3, the homogeneous-population kinship-coefficient estimator from Equation 1, and the KING-robust kinship-coefficient estimator. Results given in the table are the average of the kinship coefficients (and SDs) for each estimator calculated with 10,000 simulated random SNPs for population-structure setting 2. The following abbreviations are used: REAP, relatedness estimation in admixed populations; and SD, standard deviation.