Table 3 . The ibd segment inference results at decreasing LD levels.
| γ: | 0.0 | 0.05 | 0.1 | 1.0 | ||||
|---|---|---|---|---|---|---|---|---|
| % by mrk: | Hap. | Gen. | Hap. | Gen. | Hap. | Gen. | Hap. | Gen. |
| A. Given ibd (12%) | ||||||||
| Correct | 57.8 | 43.7 | 69.6 | 53.2 | 74.7 | 57.8 | 80.5 | 61.3 |
| Other ibd | 11.5 | 9.7 | 4.9 | 4.4 | 2.3 | 2.0 | 0.4 | 0.4 |
| False neg. | 3.5 | 10.6 | 4.5 | 12.1 | 5.6 | 13.3 | 8.0 | 17.5 |
| No call | 27.3 | 36.0 | 21.0 | 30.3 | 17.4 | 26.9 | 11.1 | 20.8 |
| B. Given no ibd (88%) | ||||||||
| Correct | 47.5 | 57.4 | 66.1 | 70.9 | 80.4 | 81.0 | 99.2 | 97.9 |
| False pos. | 17.2 | 12.1 | 8.5 | 6.5 | 3.8 | 3.4 | 0.1 | 0.1 |
| No call | 35.2 | 30.5 | 25.4 | 22.6 | 15.7 | 15.6 | 0.7 | 1.9 |
Results are shown at decreasing LD levels, that is, increasing γ, 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 involved some ibd and (B) the 88% of genome in the no-ibd state.