Table 2.
Number of Effects by Type in the Rice Genomes Based on the Invariant Sites
| Types | Count | Percentage (%) |
|---|---|---|
| 3′-UTR variant | 915 | 1.29 |
| 5′-UTR premature start codon gain variant | 91 | 0.13 |
| 5′-UTR variant | 643 | 0.91 |
| Downstream gene variant | 19,370 | 27.37 |
| Intergenic region | 1,054 | 1.49 |
| Intron variant | 1,262 | 1.78 |
| Missense variant | 26,790 | 37.86 |
| Splice acceptor variant | 228 | 0.32 |
| Splice donor variant | 313 | 0.44 |
| Splice region variant | 1,124 | 1.59 |
| Start lost | 13 | 0.02 |
| Stop gained | 916 | 1.29 |
| Stop lost | 9 | 0.01 |
| Stop retained variant | 1 | 0.00 |
| Synonymous variant | 4,201 | 5.94 |
| Upstream gene variant | 13,835 | 19.55 |
Note.—The invariant sites are the columns with no mismatches based on the multiple sequence alignments across the selected genomes that we reconstructed in this study.