Table 5.

Significant KS Test Rates

	X12-Based	X42-Based
ZP3R-ZP3 versus chr1-chr7 gene pairs	0.760	0.740
PIP5K1A-DPY19L1 versus chr1-chr7 gene pairs	0.295	0.476
ZP3R-ZP3 versus ZP3R-chr7 genes	0.818	0.811
ZP3R-ZP3 versus ZP3-chr1 genes	0.803	0.738

The proportions of significant KS tests with $\alpha =0.05$ are shown for $X_1^2$-based permutation and $X_4^2$-based permutation tests (row 1) comparing the ZP3-ZP3R results to chromosome 1–7 random gene pairs, (row 2) comparing DPY19L1-PIP5K1A to chromosome 1–7 random gene pairs, (row 3) comparing ZP3-ZP3R to ZP3R paired with chromosome 7 genes, and (row 4) comparing ZP3-ZP3R to ZP3 paired with chromosome 1 genes. All KS tests are against the alternative hypothesis that the fixed gene pair p values are more significant than the varying gene pair p values.