| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3661 | 19706 | A | G | 248 | 9331.77 | intron | Transition | 1/1 | Unannotated |
| Scaffold_3663 | 517 | C | T | 28 | 39.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3663 | 21829 | A | G | 81 | 908.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 45390 | A | G | 34 | 1105.77 | noncoding | Transition | 1/1 | Photosystem II CP47 reaction center protein (PSII 47 kDa protein) (Protein CP-47) |
| Scaffold_3664 | 16027 | A | G | 11 | 237.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3664 | 16033 | C | T | 13 | 215.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3664 | 16176 | C | T | 10 | 42.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3665 | 2925 | T | C | 16 | 120.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3669 | 7543 | T | C | 142 | 75.77 | noncoding | Transition | 0/1 | Protein Ycf2 |
| Scaffold_3669 | 23534 | A | G | 10 | 143.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3672 | 677 | G | A | 27 | 49.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 6553 | C | T | 19 | 188.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 6567 | T | C | 21 | 219.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 7170 | A | G | 14 | 168.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 7783 | G | A | 11 | 70.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 8844 | G | A | 26 | 73.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 8861 | C | T | 31 | 218.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3674 | 3937 | G | A | 31 | 657.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3674 | 3981 | C | T | 67 | 223.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3674 | 4070 | T | C | 71 | 271.77 | CDS | Transition | 0/1 | Unannotated |