| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1254 | 18135 | T | C | 13 | 380.89 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_1264 | 9270 | T | C | 21 | 40.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1265 | 52993 | T | C | 250 | 3904.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1265 | 53016 | C | T | 237 | 5827.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1265 | 53032 | C | T | 121 | 2818.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1268 | 34630 | T | C | 12 | 89.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1274 | 8363 | C | T | 30 | 219.77 | exon | Transition | 0/1 | Protein phosphatase 1 regulatory subunit INH3 (Protein INHIBITOR-3) (AtINH3) |
| Scaffold_1286 | 47484 | T | C | 16 | 120.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1289 | 17436 | A | G | 15 | 52.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1294 | 51336 | C | T | 10 | 58.77 | noncoding | Transition | 0/1 | UV-stimulated scaffold protein A homolog |
| Scaffold_1296 | 29914 | C | T | 19 | 130.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1297 | 23739 | A | G | 19 | 609.85 | CDS | Transition | 1/1 | Probable aquaporin PIP2-2 (OsPIP2;2) (Plasma membrane intrinsic protein 2-2) |
| Scaffold_1300 | 8698 | C | T | 10 | 30.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1306 | 48547 | C | T | 11 | 193.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 44089 | C | T | 150 | 2225.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 44672 | C | T | 10 | 58.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1325 | 48745 | A | G | 10 | 98.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1328 | 28676 | C | T | 14 | 46.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1347 | 786 | G | A | 15 | 33.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1361 | 31839 | C | T | 26 | 43.77 | noncoding | Transition | 0/1 | Unannotated |