| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3651 | 3506 | A | C | 62 | 215.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3532 | T | A | 64 | 1393.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 51983 | G | C | 12 | 150.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 71127 | T | G | 177 | 39.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3652 | 60367 | C | A | 13 | 423.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3652 | 63388 | A | C | 52 | 123.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3652 | 63391 | T | G | 21 | 366.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3654 | 8544 | A | C | 217 | 102.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3654 | 29796 | A | T | 17 | 547.94 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3654 | 29797 | G | T | 17 | 624.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3660 | 15682 | A | T | 241 | 2672.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3660 | 37700 | T | G | 100 | 2090.77 | noncoding | Transversion | 1/1 | Uncharacterized protein ORF91 |
| Scaffold_3660 | 38019 | G | T | 18 | 599.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3661 | 19641 | T | A | 250 | 5167.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_3663 | 12359 | T | G | 11 | 81.28 | noncoding | Transversion | 1/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3663 | 21447 | C | A | 234 | 2249.77 | exon | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21486 | C | A | 159 | 1412.77 | exon | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21643 | A | T | 24 | 376.77 | CDS | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21888 | G | C | 27 | 256.77 | CDS | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 45391 | T | A | 39 | 1201.77 | noncoding | Transversion | 1/1 | Photosystem II CP47 reaction center protein (PSII 47 kDa protein) (Protein CP-47) |