Table 1. Differential expression statistics.
| Comparison | Reads | Data | Analyzed genes | 2-fold | Binomial/G test1 | Intersect | DESeq2 |
| Parent | All | mRNA | 5,316 | 331 | 2,862 | 314 (6%) | 189 |
| Parent | All | Footprint | 5,316 | 514 | 3,057 | 490 (9%) | 145 |
| Parent | All | TE | 5,316 | 135 | 2,228 | 111 (2%) | NA |
| Parent | SNP | mRNA | 3,342 | 249 | 517 | 171 (5%) | 75 |
| Parent | SNP | Footprint | 3,342 | 475 | 671 | 289 (9%) | 67 |
| Parent | SNP | TE | 3,342 | 329 | 319 | 97 (3%) | NA |
| Hybrid | SNP | mRNA | 3,342 | 100 | 198 | 40 (1%) | 40 |
| Hybrid | SNP | Footprint | 3,342 | 194 | 210 | 67 (2%) | 70 |
| Hybrid | SNP | TE | 3,342 | 216 | 106 | 26 (1%) | 9 |
1
Bonferroni corrected p<0.05. Binomial tests were run on mRNA and footprint data. G-tests were used to test for differential TE.
2
DESeq was run on all of genes where at least one sample had more than zero counts (6,457 genes for the parent comparison using all reads and 4,361 genes for the SNP-based analyses). DESeq results were corrected for multiple testing using the Benjamini-Hochberg correction.