Table 2:
Statistics of predicted protein-coding genes
| Gene set | No. | Mean transcript length (bp) | Mean CDS length (bp) | Mean exons per gene | Mean exon length (bp) | Mean intron length (bp) | |
|---|---|---|---|---|---|---|---|
| De novo prediction | Augustus | 23,592 | 2,627.71 | 1,167.83 | 4.80 | 243.43 | 384.45 |
| GlimmerHMM | 39,985 | 5,450.51 | 747.07 | 3.14 | 238.12 | 2,200.59 | |
| SNAP | 24,882 | 2,876.50 | 728.45 | 4.22 | 172.73 | 667.66 | |
| Geneid | 33,780 | 3,829.40 | 899.99 | 4.44 | 202.74 | 851.78 | |
| Genscan | 21,882 | 8,251.09 | 1,355.87 | 6.34 | 213.98 | 1,292.13 | |
| Homolog prediction | Pyrus bretschneideri | 20,265 | 3,119.83 | 1,356.17 | 4.74 | 286.35 | 472.06 |
| Malus domestica | 20,010 | 2,920.17 | 1,361.30 | 4.65 | 292.56 | 426.72 | |
| Prunus mume | 23,064 | 3,038.66 | 1,346.19 | 4.78 | 281.67 | 447.84 | |
| Prunus persica | 28,915 | 2,296.51 | 1,099.56 | 4.06 | 270.55 | 390.64 | |
| Arabidopsis thaliana | 28,284 | 2,071.73 | 973.28 | 3.67 | 265.51 | 412.07 | |
| Fragaria vesca | 22,927 | 2,994.24 | 1,380.61 | 4.59 | 300.66 | 449.24 | |
| Prunus avium | 22,715 | 3,077.20 | 1,351.28 | 4.74 | 284.86 | 461.03 | |
| RNA-seq | PASA | 196,264 | 3,913.86 | 1,008.68 | 5.16 | 195.60 | 698.88 |
| Transcripts | 42,450 | 11,076.28 | 2,360.92 | 6.85 | 344.83 | 1,490.64 | |
| EVM | 27,981 | 2,736.70 | 1,061.73 | 4.57 | 232.52 | 469.68 | |
| PASA-update* | 27,594 | 2,784.15 | 1,092.82 | 4.64 | 235.59 | 464.83 | |
| Final set* | 24,448 | 2,988.45 | 1,157.42 | 4.97 | 233.09 | 461.72 | |
*
Includes untranslated regions. CDS: coding sequence.