| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_458 | 22569 | G | A | 39 | 59.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_458 | 29690 | A | G | 159 | 1402.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 5 (eIF-5) |
| Scaffold_458 | 30077 | C | T | 158 | 4101.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 5 (eIF-5) |
| Scaffold_458 | 30238 | A | G | 250 | 831.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 5 (eIF-5) |
| Scaffold_458 | 30332 | G | A | 250 | 3516.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 5 (eIF-5) |
| Scaffold_458 | 30398 | T | C | 250 | 7027.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 5 (eIF-5) |
| Scaffold_458 | 30548 | T | C | 250 | 1117.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 5 (eIF-5) |
| Scaffold_463 | 20848 | A | G | 91 | 155.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_463 | 22477 | A | G | 41 | 885.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_463 | 22478 | C | T | 43 | 893.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_464 | 10743 | A | G | 10 | 88.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_464 | 45633 | A | G | 20 | 181.77 | intron | Transition | 0/1 | (3S,6E)-nerolidol synthase 2, chloroplastic/mitochondrial (FaNES2) (EC 4.2.3.48) |
| Scaffold_464 | 46015 | A | G | 20 | 173.77 | intron | Transition | 0/1 | Myrcene synthase, chloroplastic (EC 4.2.3.15) |
| Scaffold_465 | 66679 | A | G | 47 | 1028.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_476 | 60306 | C | T | 31 | 509.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_485 | 2885 | G | A | 11 | 247.98 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_485 | 2898 | T | C | 11 | 244.84 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_485 | 13101 | T | C | 39 | 48.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_487 | 32482 | T | C | 21 | 35.77 | CDS | Transition | 0/1 | Protein argonaute 4A (OsAGO4a) |
| Scaffold_493 | 63855 | G | A | 14 | 331.85 | noncoding | Transition | 0/1 | Unannotated |