Table 6.
Comparison of the Effect of Long-Range LD Regions of Varying Lengths on SMARTPCA and SPA
| Method | Inversion Length (SNPs) | Euclidean Distance: 2nd[1st, 3rd] Quartile | Distance: 2nd[1st, 3rd] Quartile (km) | Relative to Length 0 |
|---|---|---|---|---|
| SMARTPCA pruned | 0 | 2.78 [1.67, 4.61] | 247.1 [155.0, 378.3] | 1 |
| SMARTPCA pruned | 410 | 3.18 [1.84, 5.30] | 275.7 [162.7, 433.4] | 1.12 |
| SMARTPCA pruned | 1,800 (whole) | 6.98 [4.18, 11.9] | 545.4 [362.6, 832.9] | 2.21 |
| SPA pruned | 0 | 2.55 [1.56, 4.02] | 226.4 [137.7, 336.2] | 1 |
| SPA pruned | 450 | 2.60 [1.58, 4.03] | 227.3 [139.5, 336.8] | 1.00 |
| SPA pruned | 900 | 2.63 [1.58, 4.09] | 230.3 [139.4, 344.6] | 1.02 |
| SPA pruned | 1,800 (whole) | 2.73 [1.61, 4.23] | 240.6 [141.8, 355.7] | 1.06 |
The genotypes of the Spanish samples from the chromosome 8 inversion were excised, trimmed to different lengths, and “transplanted” in the genotypes of the POPRES samples. “Inversion length” gives the number of SNPs in the transplanted inversion out of the entire 1,800 SNPs in the inversion region. Reported error measures are the same as in Table 1. “Relative to Length 0” gives, per method, the ratio between the median error (in km) and the result before the inversion was added.