| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2561 | 35461 | G | T | 72 | 87.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2562 | 20213 | T | G | 29 | 490.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2562 | 21116 | A | T | 14 | 97.77 | CDS | Transversion | 0/1 | Protein VAC14 homolog |
| Scaffold_2562 | 21403 | C | G | 12 | 156.77 | exon | Transversion | 0/1 | Protein VAC14 homolog |
| Scaffold_2563 | 12210 | G | C | 10 | 141.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2565 | 85787 | G | T | 23 | 318.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2565 | 86392 | T | A | 26 | 33.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2565 | 86482 | A | C | 12 | 43.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2565 | 86487 | T | G | 14 | 83.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2569 | 42534 | T | A | 14 | 107.77 | noncoding | Transversion | 0/1 | WAT1-related protein At4g19185 |
| Scaffold_2570 | 33208 | C | G | 17 | 252.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2570 | 61360 | G | T | 53 | 1019.77 | CDS | Transversion | 0/1 | Cell division cycle 20.1, cofactor of APC complex (AtCDC20.1) |
| Scaffold_2570 | 61372 | T | A | 64 | 1359.77 | CDS | Transversion | 0/1 | Cell division cycle 20.1, cofactor of APC complex (AtCDC20.1) |
| Scaffold_2571 | 13911 | G | T | 11 | 135.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2571 | 13926 | T | G | 15 | 236.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2573 | 139 | T | G | 37 | 751.77 | CDS | Transversion | 0/1 | Cellulose synthase-like protein B2 (AtCslB2) (EC 2.4.1.-) |
| Scaffold_2573 | 224 | T | A | 98 | 1119.77 | CDS | Transversion | 0/1 | Cellulose synthase-like protein H1 (EC 2.4.1.-) (OsCslH1) |
| Scaffold_2573 | 557 | T | G | 22 | 218.77 | CDS | Transversion | 0/1 | Cellulose synthase-like protein H1 (EC 2.4.1.-) (OsCslH1) |
| Scaffold_2576 | 58701 | G | T | 22 | 140.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2580 | 13119 | T | A | 19 | 144.77 | intron | Transversion | 0/1 | DNA-binding protein BIN4 (Protein BRASSINOSTEROID INSENSITIVE 4) (Protein MIDGET) |