Table 2.
Regions for which the AfAdm map differs most from a 80%:20% average of the HapMapYRI and HapMapCEU maps. Regions where the AfAdm map has lower rate estimates are shown at top, followed by regions where the AfAdm map has higher rates.
| Chr. | Positiona | Differenceb | Structural variations |
|---|---|---|---|
| 8 | 11.4–13.3 | −1.93 | 4.7-Mb inversion29,30 |
| 9 | 37.6–39.5 | −1.04 | 36-kb inversion32/8-Mb CNV33 |
| 10 | 124.9–126.8 | −1.00 | |
| 16 | 21.7–23.5 | −0.89 | 1.1-Mb inversion39 |
| 7 | 5.1–6.4 | −0.87 | 1-Mb inversion39,41 |
| 22 | 24.5–26.9 | 1.42 | 500-kb CNV33,42,43 |
| 8 | 133.8–135.6 | 1.30 | |
| 16 | 81.1–83.0 | 1.23 | 1-kb inversion41 |
| 22 | 34.8–36.5 | 1.23 | |
| 14 | 45.9–47.6 | 1.20 | 1-Mb CNV42 |
| 8 | 7.2–9.1 | 1.10 | 4.7-Mb inversion29,30 |
| 18 | 22.1–23.7 | 1.04 | |
| 3 | 51.4–54.3 | 1.03 | 45-kb inversion32,44 |
| 14 | 93.3–95.1 | 1.03 | 1-kb inversion45 |
| 14 | 43.2–44.9 | 1.03 | 1-Mb CNV46 |
| 2 | 59.8–63.3 | 1.03 | 2.9-Mb CNV33 |
| 15 | 67.6–68.9 | 0.99 | |
| 5 | 30.6–32.2 | 0.99 | |
| 14 | 50.9–52.1 | 0.97 | |
| 16 | 64.0–65.4 | 0.97 | |
| 6 | 16.1–18.4 | 0.96 | |
| 10 | 72.5–74.0 | 0.94 | 36-kb inversion32/1.2-Mb CNV47 |
| 9 | 6.8–8.1 | 0.91 | |
| 8 | 23.1–24.4 | 0.88 | 2.5-Mb CNV33 |
| 7 | 102.7–104.1 | 0.84 |
To identify the regions, we identified the top 1% of the intervals with the greatest difference between the AfAdm map and the HapMapYRI and HapMapCEU maps computed on 1-Mb intervals spaced every 50 kb. We joined intervals whose endpoints were not more than 1-Mb apart from each other, and we examined and present here only regions supported by at least five intervals. We omitted seven regions where visual inspection revealed that the difference was not caused by the AfAdm rate but rather by the HapMapYRi rate (Supplementary Table 3). The reported structural variations were observed in surveys of structural variations in random samples of European or African individuals and were not further than 1-Mb away from the focus regions. in addition, CNVs had to be at least 500 kb in length to be included, and we only report here the largest CNV in the region. The intervals before collapsing the data are shown in Supplementary Figure 10.
Position in Mb.
Largest difference per region, given in cM. Negative values imply lower rates in the AfAdm map. Chr., chromosome; CNV, copy number variation.