| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_494 | 1621 | T | C | 19 | 80.77 | CDS | Transition | 0/1 | Obg-like ATPase 1 (Ribosome-binding ATPase YchF) (OsYchF1) |
| Scaffold_495 | 51518 | T | C | 15 | 37.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_496 | 9684 | T | C | 56 | 781.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_496 | 26478 | G | A | 41 | 546.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_497 | 4331 | A | G | 12 | 49.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_498 | 25986 | G | A | 27 | 686.82 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_498 | 26004 | A | G | 11 | 263.22 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_501 | 53064 | A | G | 32 | 957.77 | intron | Transition | 1/1 | Unannotated |
| Scaffold_501 | 53628 | C | T | 36 | 1039.74 | intron | Transition | 0/1 | Metallothionein-like protein type 2 |
| Scaffold_501 | 53629 | A | G | 62 | 1993.77 | intron | Transition | 1/1 | Metallothionein-like protein type 2 |
| Scaffold_502 | 66071 | C | T | 11 | 334.22 | intron | Transition | 0/1 | Unannotated |
| Scaffold_504 | 59847 | G | A | 10 | 70.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_505 | 40911 | C | T | 13 | 336.56 | exon | Transition | 0/1 | Unannotated |
| Scaffold_509 | 21094 | C | T | 17 | 30.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_523 | 28466 | T | C | 14 | 52.77 | exon | Transition | 0/1 | Calcium-transporting ATPase 4, plasma membrane-type (EC 7.2.2.10) (Ca(2+)-ATPase isoform 4) |
| Scaffold_523 | 28566 | G | A | 13 | 132.77 | exon | Transition | 0/1 | Calcium-transporting ATPase 4, plasma membrane-type (EC 7.2.2.10) (Ca(2+)-ATPase isoform 4) |
| Scaffold_523 | 49303 | T | C | 250 | 4144.77 | CDS | Transition | 0/1 | Calnexin homolog |
| Scaffold_523 | 49378 | A | G | 244 | 735.77 | CDS | Transition | 0/1 | Calnexin homolog |
| Scaffold_523 | 49408 | T | C | 118 | 1333.77 | CDS | Transition | 0/1 | Calnexin homolog |
| Scaffold_523 | 49414 | A | G | 116 | 909.77 | CDS | Transition | 0/1 | Calnexin homolog |