| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1503 | 45617 | T | C | 79 | 221.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1505 | 21024 | T | C | 24 | 298.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1505 | 21036 | T | C | 24 | 189.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1505 | 21064 | A | G | 60 | 50.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1508 | 41369 | T | A,G | 15 | 1278.77 | noncoding | Transition | 1/2 | Unannotated |
| Scaffold_1509 | 34831 | T | C | 12 | 45.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1525 | 16854 | A | G | 10 | 64.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1527 | 7320 | T | C | 43 | 310.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1527 | 7323 | C | T | 56 | 49.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1531 | 26963 | A | G | 19 | 51.77 | exon | Transition | 0/1 | Transcription elongation factor SPT6 homolog (AtSPT6) |
| Scaffold_1538 | 44889 | C | T | 43 | 778.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1543 | 7280 | C | T | 12 | 252.74 | noncoding | Transition | 0/1 | UDP-glycosyltransferase 83A1 (EC 2.4.1.-) |
| Scaffold_1544 | 14255 | T | C | 11 | 125.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1547 | 17925 | T | C | 25 | 96.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1565 | 31863 | A | G | 22 | 31.77 | exon | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit K (eIF3k) (eIF-3 p25) |
| Scaffold_1566 | 13579 | T | C | 139 | 458.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1576 | 26429 | A | G | 36 | 269.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1576 | 26602 | T | C | 17 | 61.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1583 | 943 | A | G | 50 | 179.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1585 | 5420 | A | G | 22 | 275.77 | CDS | Transition | 0/1 | Heat shock 70 kDa protein BIP1 (Luminal-binding protein 1) (OsBiP1) |