Table 3.
Summary of predicted protein-coding genes in P. campanulata.
| Approach | Software/species | Number | Average gene length (bp) | Average CDS length per gene(bp) | Average exons per gene | Average exon length (bp) | Average intron length (bp) |
|---|---|---|---|---|---|---|---|
| De novo | Augustus | 26,465 | 2,411.79 | 1,111.79 | 1,111.79 | 257.89 | 392.62 |
| GlimmerHMM | 41,528 | 5,139.14 | 727.59 | 727.59 | 257.53 | 2,416.99 | |
| SNAP | 35,394 | 3,845.62 | 737.17 | 737.17 | 204.91 | 1,196.70 | |
| Geneid | 31,387 | 3,804.80 | 957.03 | 957.03 | 212.45 | 812.56 | |
| Genscan | 20,821 | 8,384.80 | 1,425.22 | 1,425.22 | 212.31 | 1,218.20 | |
| Homolog | Malus domestica | 25,812 | 3,059.67 | 1,066.69 | 4.05 | 263.48 | 653.75 |
| Cerasus serrulata | 32,363 | 2,373.10 | 1,049.06 | 4.01 | 261.62 | 439.88 | |
| Vitis vinifera | 21,391 | 2,630.94 | 1,123.75 | 4.34 | 259.20 | 451.87 | |
| Arabidopsis thaliana | 24,423 | 2,263.16 | 1,067.89 | 3.84 | 278.21 | 421.11 | |
| Prunus salicina | 32,443 | 2,083.57 | 1,000.06 | 3.81 | 262.51 | 385.64 | |
| Prunus yedoensis | 35,622 | 1,795.22 | 806.52 | 3.51 | 229.91 | 394.23 | |
| RNA-Seq | Cufflinks | 53,655 | 6,750.99 | 2,297.48 | 6.53 | 351.96 | 805.68 |
| PASA | 62,247 | 2,799.00 | 1,073.49 | 4.86 | 220.81 | 446.85 | |
| EVM | 29,352 | 2,406.14 | 1,081.29 | 4.35 | 248.85 | 396.04 | |
| PASA-update | 29,189 | 2,419.83 | 1,100.36 | 4.38 | 250.96 | 389.84 | |
| Final set | 24,861 | 2,639.37 | 1,180.73 | 4.79 | 246.40 | 384.67 |