| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1585 | 5456 | T | C | 12 | 133.77 | CDS | Transition | 0/1 | Heat shock 70 kDa protein BIP1 (Luminal-binding protein 1) (OsBiP1) |
| Scaffold_1589 | 33427 | A | G | 66 | 212.77 | noncoding | Transition | 0/1 | Copper transport protein CCH (Copper chaperone CCH) |
| Scaffold_1592 | 42201 | T | C | 11 | 192.98 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1593 | 18105 | T | C | 98 | 244.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1609 | 26892 | A | G | 13 | 274.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1615 | 44643 | A | G | 24 | 283.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1616 | 29343 | C | T | 43 | 812.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1626 | 39112 | G | A | 31 | 282.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1649 | 32516 | A | G | 89 | 218.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1649 | 32553 | C | T | 41 | 106.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1654 | 40730 | G | A | 78 | 649.77 | noncoding | Transition | 0/1 | Expansin-A5 (AtEXPA5) (Alpha-expansin-5) (At-EXP5) (AtEx5) (Ath-ExpAlpha-1.4) |
| Scaffold_1654 | 40937 | C | T | 68 | 589.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1654 | 40957 | T | C | 44 | 466.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1660 | 12863 | A | G | 12 | 277.9 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1660 | 12874 | T | C | 12 | 254.9 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1666 | 15537 | A | G | 142 | 706.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1668 | 7085 | A | G | 117 | 150.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1668 | 7086 | A | G | 119 | 2476.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1670 | 133 | A | G | 16 | 63.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1688 | 13158 | A | G | 14 | 153.41 | noncoding | Transition | 0/1 | Unannotated |