| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2588 | 61338 | A | G | 250 | 59.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2591 | 26518 | C | T | 16 | 248.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2591 | 58834 | C | T | 12 | 149.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2593 | 73184 | C | T | 61 | 311.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2593 | 73265 | A | G | 42 | 210.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2596 | 56651 | C | T | 44 | 117.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2597 | 1969 | A | G | 32 | 35.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2598 | 54797 | A | G | 142 | 1244.77 | CDS | Transition | 0/1 | B3 domain-containing protein REM19 (Protein RELATED TO VERNALIZATION 1) (Protein REPRODUCTIVE MERISTEM 19) |
| Scaffold_2598 | 59359 | A | G | 10 | 73.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2598 | 59362 | A | G | 10 | 84.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2599 | 45482 | T | C | 10 | 227.18 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2602 | 19598 | A | G | 46 | 796.77 | CDS | Transition | 0/1 | Two-component response regulator ORR21 (OsRRB1) |
| Scaffold_2605 | 34563 | C | T | 92 | 2268.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2605 | 35172 | C | T | 15 | 346.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2607 | 9205 | A | G | 17 | 39.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2611 | 34245 | A | G | 18 | 66.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2612 | 3269 | T | C | 33 | 213.77 | intron | Transition | 0/1 | Probable ethanolamine kinase (EC 2.7.1.82) (Protein EMBRYO DEFECTIVE 1187) |
| Scaffold_2618 | 26144 | T | C | 34 | 181.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2618 | 41385 | A | G | 15 | 33.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2621 | 63723 | A | G | 42 | 49.77 | noncoding | Transition | 0/1 | Methyl-CpG-binding domain protein 4-like protein (EC 3.2.2.-) (Protein MBD4-like) |