| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3650 | 49299 | C | A | 216 | 1476.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3400 | A | C | 22 | 486.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3446 | G | T | 48 | 653.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3506 | A | C | 30 | 233.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3532 | T | A | 27 | 607.79 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3652 | 63388 | A | C | 40 | 196.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3652 | 63389 | C | A | 40 | 193.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3660 | 15682 | A | T | 238 | 2942.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3660 | 15786 | A | C | 250 | 195.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 5704 | A | C | 10 | 30.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 21302 | G | T | 10 | 64.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 21304 | A | T | 11 | 101.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3663 | 21447 | C | A | 239 | 860.77 | exon | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21486 | C | A | 144 | 290.77 | exon | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21643 | A | T | 17 | 166.77 | CDS | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21888 | G | C | 11 | 52.77 | CDS | Transversion | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 22792 | A | T | 12 | 287.18 | CDS | Transversion | 0/1 | Novel plant SNARE 12 (AtNPSN12) |
| Scaffold_3665 | 2926 | A | C | 25 | 31.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3672 | 1966 | T | A | 71 | 36.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3673 | 6525 | A | T | 12 | 69.77 | CDS | Transversion | 0/1 | Unannotated |