| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2521 | 90229 | T | C | 27 | 346.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2523 | 6707 | C | T | 12 | 55.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2524 | 10893 | C | T | 12 | 36.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2525 | 89271 | T | C | 12 | 312.03 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2525 | 89279 | T | C | 14 | 348.28 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2525 | 89318 | G | A | 39 | 31.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2528 | 19286 | C | T | 11 | 42.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2535 | 66325 | T | C | 15 | 70.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2536 | 104417 | A | G | 10 | 55.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2538 | 36849 | A | G | 21 | 40.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2538 | 36850 | G | A | 21 | 43.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2538 | 65680 | A | G | 23 | 34.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2543 | 10763 | A | G | 13 | 70.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2546 | 7358 | A | G | 12 | 39.77 | CDS | Transition | 0/1 | Tyrosine/DOPA decarboxylase 5 [Includes: DOPA decarboxylase (DDC) (EC 4.1.1.28); Tyrosine decarboxylase (EC 4.1.1.25)] |
| Scaffold_2546 | 104350 | A | G | 14 | 39.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2548 | 41006 | C | T | 90 | 435.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2549 | 35628 | G | A | 11 | 36.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2550 | 16546 | T | C | 21 | 40.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2550 | 57759 | T | C | 41 | 86.77 | CDS | Transition | 0/1 | Alpha-1,4 glucan phosphorylase L-2 isozyme, chloroplastic/amyloplastic (EC 2.4.1.1) (Starch phosphorylase L-2) |
| Scaffold_2553 | 41610 | A | G | 63 | 179.77 | CDS | Transition | 0/1 | UPF0603 protein OsI_019212, chloroplastic |