Table 1.
Coefficients of partial determination of regional variation in nucleotide substitution and the proportion of variation explained by each model (at a 1-Megabase scale)
| Predictors/models | Fixed nucleotide substitution (FNS) frequency | Single nucleotide polymorphism (SNP) frequency |
|---|---|---|
| G4 weighted coveragea | 1.04% | 1.08% |
| A-phased repeats coverage | 0.50% | 0.10% |
| Inverted repeats coverage | 0.48% | 0.68% |
| Direct repeats coverage | 1.63% | 8.01% |
| Z-DNA motifs coverage | 2.32% | 0.66% |
| Mirror repeats coverage | 0.47% | 0.27% |
| All non-B | 15.94% | 19.95% |
| Replication timing | 2.08% | 0.54% |
| Recombination rate | 0.65% | 6.12% |
| DNase hypersensitive sites coverage | 0.12% | 1.08% |
| RNA polymerase II binding sites coverage | 0.49% | 0.66% |
| CHH methylation coverage | 0.29% | 0.01% |
| CpG island coverage | 0.67% | 0.35% |
| Lamina Associated Domains coverage | 1.35% | 0.72% |
| Distance to telomere | 15.25% | 14.19% |
| Distance to centromere | 0.76% | 3.45% |
| H2AFZ signal | 0.29% | 0.39% |
| H3K27me3 signal | 0.00% | 0.14% |
| H3K36me3 signal | 0.38% | 0.12% |
| H3K9ac signal | 0.15% | 0.27% |
| H3K9me3 signal | 1.72% | 1.52% |
| Telomere hexamer presence | 0.28% | 0.02% |
| R-squared | 58.00% | 55.61% |
aCoverage of G4 loci was weighted by their stability.