Table 2. Augmented ANOVA table for SNP-Centered PCA of SNP data on oats, using SNP coding rare = 1.
PCA is applied to Individual main effects and S×I interaction effects combined (I&S×I), and the portion of each is shown in the last two columns.
| Source | df | SS | Individuals | SxI |
|---|---|---|---|---|
| Total | 851534 | 157442.756 | ||
| SNPs | 1340 | 16872.731 | ||
| I&SxI | 850194 | 140570.025 | 2077.808 | 138492.217 |
| PC1 | 1974 | 16325.612 | 857.676 | 15467.936 |
| PC2 | 1972 | 9751.158 | 257.217 | 9493.941 |
| PC3 | 1970 | 6250.504 | 423.134 | 5827.370 |
| PC4 | 1968 | 4860.910 | 23.386 | 4837.524 |
| PC5 | 1966 | 3510.312 | 4.521 | 3505.791 |
| PC6 | 1964 | 3181.953 | 187.615 | 2994.338 |
| PC7 | 1962 | 2891.656 | 1.654 | 2890.002 |
| Residual | 836418 | 93797.920 | 322.606 | 93475.314 |