| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2451 | 116961 | A | C | 40 | 697.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2453 | 24857 | A | T | 14 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2455 | 55897 | A | C | 12 | 58.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2455 | 77115 | C | G | 19 | 435.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2455 | 77249 | G | T | 11 | 89.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2455 | 78207 | T | A | 51 | 361.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2455 | 78942 | T | A | 24 | 174.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2456 | 44872 | T | A | 54 | 1399.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2456 | 113127 | T | A | 56 | 691.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2463 | 38175 | T | G | 19 | 34.77 | CDS | Transversion | 0/1 | Probable leucine-rich repeat receptor-like protein kinase At5g49770 (EC 2.7.11.1) |
| Scaffold_2463 | 82595 | G | T | 25 | 853.77 | intron | Transversion | 1/1 | Peroxidase 21 (Atperox P21) (EC 1.11.1.7) (ATP2a/ATP2b) (PRXR5) |
| Scaffold_2463 | 84295 | T | A | 15 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2463 | 84296 | C | G | 15 | 46.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2464 | 107 | C | A | 32 | 46.74 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_2464 | 59687 | A | T | 15 | 43.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2471 | 105633 | A | C | 12 | 95.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2471 | 105634 | G | T | 13 | 135.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2474 | 57958 | T | G | 23 | 31.77 | CDS | Transversion | 0/1 | Calcium-dependent protein kinase 19 (OsCDPK19) (OsCPK19) (EC 2.7.11.1) (Calcium-dependent protein kinase isoform 2) (OsCDPK2) (OsCPK2) |
| Scaffold_2475 | 121718 | T | A | 56 | 1612.77 | intron | Transversion | 0/1 | Elongation factor 1-alpha (EF-1-alpha) |
| Scaffold_2475 | 122073 | T | A | 250 | 987.77 | CDS | Transversion | 0/1 | Elongation factor 1-alpha (EF-1-alpha) |