| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3635 | 18036 | A | C | 20 | 248.77 | CDS | Transversion | 0/1 | CLIP-associated protein (AtCLASP) |
| Scaffold_3635 | 18045 | T | A | 16 | 55.77 | CDS | Transversion | 0/1 | CLIP-associated protein (AtCLASP) |
| Scaffold_3635 | 18087 | T | G | 14 | 146.77 | CDS | Transversion | 0/1 | CLIP-associated protein (AtCLASP) |
| Scaffold_3641 | 2260 | C | A | 15 | 195.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3641 | 2277 | A | T | 15 | 183.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3641 | 2584 | G | T | 51 | 433.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3641 | 13597 | A | T | 12 | 198.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3345 | G | C | 13 | 80.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3400 | A | C | 83 | 2036.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3446 | G | T | 98 | 1400.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3506 | A | C | 76 | 1023.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3532 | T | A | 92 | 1983.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3656 | 36844 | C | A | 14 | 159.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 21304 | A | T | 23 | 392.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 21447 | C | A | 246 | 2382.77 | exon | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21486 | C | A | 188 | 1061.77 | exon | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21643 | A | T | 42 | 383.77 | CDS | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21888 | G | C | 139 | 1383.77 | CDS | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21899 | A | T | 13 | 115.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 22792 | A | T | 52 | 586.77 | CDS | Transversion | 0/1 | Novel plant SNARE 12 (AtNPSN12) |