Table 2.
Significance of clinal and seasonal frequency changes of SNPs that are associated with egg retention (P < 10 − 5). The effect (N–S) column shows the effect of each SNP on egg retention time, calculated as ½ (North Allele mean – South Allele mean). If effect (N–S) is greater than 0, then egg retention time is longer in the north vs. south.
| Chr | Pos | MAF | Gene | Class | Season q-value | Clinal q-value | North allele | South allele | Effect (N–S) |
|---|---|---|---|---|---|---|---|---|---|
| 3R | 22722373 | 0.446 | T48 | Intronic | 0.953 | 0.025 | T | C | 0.105 |
| 3R | 23759237 | 0.302 | Mes-4 | Intronic | 0.947 | 0.016 | A | T | 0.124 |
| 3R | 27115805 | 0.333 | NA | NA | 0.788 | 0.001 | C | T | 0.109 |
| 3L | 16448208 | 0.216 | CG33158 | Intronic | 0.939 | 0.665 | – | – | – |
| 3L | 1696552 | 0.218 | CG7991 | Intronic | 0.992 | 0.236 | – | – | – |
| X | 3655147 | 0.144 | tlk | Intronic | 0.966 | 0.799 | – | – | – |
| X | 22397621 | 0.364 | StnA/B | 5’ UTR | 0.954 | 0.044 | T | C | −0.112 |