| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1216 | 613 | C | G | 12 | 61.77 | CDS | Transversion | 0/1 | DEAD-box ATP-dependent RNA helicase 7 (EC 3.6.4.13) |
| Scaffold_1229 | 36386 | T | A | 11 | 103.77 | intron | Transversion | 0/1 | Secretory carrier-associated membrane protein 5 (Secretory carrier membrane protein 5) |
| Scaffold_1230 | 18332 | A | T | 36 | 865.84 | noncoding | Transversion | 0/1 | Deacetoxyvindoline 4-hydroxylase (EC 1.14.11.20) |
| Scaffold_1231 | 51360 | T | A | 11 | 151.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1241 | 52549 | A | T | 42 | 559.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1241 | 52550 | C | G | 56 | 1035.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1243 | 23570 | G | T | 29 | 573.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1248 | 3845 | T | A | 10 | 167.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1250 | 20254 | T | A | 10 | 125.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1257 | 32923 | G | T | 41 | 701.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1257 | 33521 | T | A | 38 | 261.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1257 | 33522 | G | T | 35 | 94.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1262 | 33197 | C | A | 36 | 57.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1268 | 34632 | A | C | 65 | 595.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1269 | 50438 | T | A | 11 | 50.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1276 | 35377 | T | G | 11 | 117.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1278 | 2858 | G | T | 75 | 713.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1285 | 23751 | A | C | 13 | 302.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1297 | 23741 | G | T | 16 | 272.77 | CDS | Transversion | 0/1 | Probable aquaporin PIP2-2 (OsPIP2;2) (Plasma membrane intrinsic protein 2-2) |
| Scaffold_1300 | 20060 | A | C | 40 | 594.77 | intron | Transversion | 0/1 | Unannotated |