| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_244 | 11819 | A | C | 14 | 57.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_244 | 55850 | T | A | 14 | 103.77 | exon | Transversion | 0/1 | Zinc finger CCCH domain-containing protein 40 (OsC3H40) |
| Scaffold_244 | 56443 | A | C | 37 | 98.77 | CDS | Transversion | 0/1 | Zinc finger CCCH domain-containing protein 40 (OsC3H40) |
| Scaffold_244 | 56458 | C | A | 39 | 107.77 | CDS | Transversion | 0/1 | Zinc finger CCCH domain-containing protein 40 (OsC3H40) |
| Scaffold_246 | 35234 | T | G | 12 | 277.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_248 | 1107 | A | C | 17 | 316.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_251 | 85015 | C | G | 10 | 325.78 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_254 | 33610 | A | C | 250 | 213.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_256 | 39483 | A | T | 19 | 91.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_256 | 39506 | C | G | 15 | 143.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_264 | 1599 | T | G | 29 | 690.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_264 | 79792 | T | G | 12 | 397.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_273 | 28586 | A | C | 14 | 126.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_275 | 3261 | C | A | 16 | 52.77 | CDS | Transversion | 0/1 | Homeobox-DDT domain protein RLT2 (Protein RINGLET 2) |
| Scaffold_275 | 51171 | T | G | 11 | 298.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_280 | 5625 | C | G | 16 | 489.1 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_285 | 22854 | C | G | 12 | 347.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_289 | 27177 | A | T | 39 | 1071.77 | intron | Transversion | 1/1 | F-box protein SKIP23 (SKP1-interacting partner 23) |
| Scaffold_289 | 35661 | T | A | 16 | 498.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_296 | 22104 | A | T | 90 | 248.77 | noncoding | Transversion | 0/1 | BTB/POZ domain-containing protein At2g30600 |