| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2495 | 104337 | T | C | 19 | 58.77 | exon | Transition | 0/1 | U-box domain-containing protein 30 (EC 2.3.2.27) (Plant U-box protein 30) (RING-type E3 ubiquitin transferase PUB30) |
| Scaffold_2498 | 49868 | G | A | 15 | 73.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2498 | 105731 | T | C | 14 | 155.77 | exon | Transition | 0/1 | Transcription termination factor MTERF15, mitochondrial (Mitochondrial transcription termination factor 15) |
| Scaffold_2498 | 105758 | G | A | 10 | 82.77 | exon | Transition | 0/1 | Transcription termination factor MTERF15, mitochondrial (Mitochondrial transcription termination factor 15) |
| Scaffold_2498 | 106032 | G | A | 11 | 64.77 | exon | Transition | 0/1 | Transcription termination factor MTERF15, mitochondrial (Mitochondrial transcription termination factor 15) |
| Scaffold_2500 | 11624 | C | T | 12 | 64.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2500 | 56660 | T | C | 28 | 644.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2500 | 56661 | T | C | 25 | 587.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2501 | 69882 | A | G | 32 | 254.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2501 | 71852 | A | G | 24 | 46.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2501 | 78028 | T | C | 17 | 80.77 | exon | Transition | 0/1 | Protein disulfide isomerase-like 2-2 (OsPDIL2-2) (EC 5.3.4.1) (Protein disulfide isomerase-like 4-2) (OsPDIL4-2) |
| Scaffold_2502 | 85041 | A | G | 22 | 30.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2505 | 5251 | G | A | 10 | 55.77 | CDS | Transition | 0/1 | SART-1 family protein DOT2 (Protein DEFECTIVELY ORGANIZED TRIBUTARIES 2) (Protein MERISTEM-DEFECTIVE) |
| Scaffold_2505 | 47960 | T | C | 40 | 33.77 | CDS | Transition | 0/1 | CBS domain-containing protein CBSX5 |
| Scaffold_2506 | 33450 | T | C | 15 | 46.77 | exon | Transition | 0/1 | Adenylosuccinate synthetase 2, chloroplastic (AMPSase 2) (AdSS 2) (EC 6.3.4.4) (IMP--aspartate ligase 2) |
| Scaffold_2506 | 65073 | G | A | 13 | 61.77 | exon | Transition | 0/1 | Probable galacturonosyltransferase-like 3 (EC 2.4.1.-) |
| Scaffold_2507 | 13884 | G | A | 19 | 37.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2507 | 107404 | A | G | 97 | 108.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2519 | 104764 | A | G | 14 | 43.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2519 | 105132 | C | T | 12 | 320.77 | intron | Transition | 0/1 | Unannotated |