| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2586 | 89693 | T | C | 56 | 39.77 | CDS | Transition | 0/1 | T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta) (Chaperonin CCT2) |
| Scaffold_2589 | 83093 | T | C | 20 | 550.94 | exon | Transition | 1/1 | Unannotated |
| Scaffold_2590 | 55002 | A | G | 11 | 107.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2590 | 92112 | C | T | 20 | 49.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2598 | 54797 | A | G | 24 | 571.41 | CDS | Transition | 1/1 | B3 domain-containing protein REM19 (Protein RELATED TO VERNALIZATION 1) (Protein REPRODUCTIVE MERISTEM 19) |
| Scaffold_2604 | 46462 | G | A | 12 | 61.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2606 | 26278 | G | A | 15 | 33.77 | exon | Transition | 0/1 | Histone-lysine N-methyltransferase ATXR3 (EC 2.1.1.43) (Protein SET DOMAIN GROUP 2) (Trithorax-related protein 3) (TRX-related protein 3) |
| Scaffold_2607 | 18864 | A | G | 16 | 40.77 | CDS | Transition | 0/1 | Chorismate mutase 2 (AtCM2) (EC 5.4.99.5) (CM-2) |
| Scaffold_2608 | 52945 | T | C | 20 | 31.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2611 | 28305 | A | G | 12 | 55.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2616 | 51171 | T | C | 31 | 669.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2624 | 66925 | G | A | 15 | 43.77 | exon | Transition | 0/1 | Calcium-dependent protein kinase 25 (OsCDPK25) (OsCPK25) (EC 2.7.11.1) |
| Scaffold_2632 | 86679 | G | A | 12 | 132.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2633 | 43110 | T | C | 86 | 116.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2633 | 43111 | T | C | 107 | 32.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2640 | 66045 | A | G | 17 | 282.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2645 | 57519 | A | G | 28 | 34.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2646 | 49370 | C | T | 33 | 39.77 | exon | Transition | 0/1 | Probable splicing factor 3A subunit 1 |
| Scaffold_2646 | 49774 | A | G | 17 | 46.77 | exon | Transition | 0/1 | Probable splicing factor 3A subunit 1 |
| Scaffold_2646 | 51483 | A | G | 14 | 89.77 | exon | Transition | 0/1 | Probable splicing factor 3A subunit 1 |