| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_389 | 9962 | A | C | 52 | 381.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_389 | 9964 | T | G | 37 | 168.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_391 | 21300 | C | A | 12 | 100.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_400 | 9432 | A | T | 13 | 452.77 | intron | Transversion | 1/1 | Metacaspase-5 (AtMC5) (EC 3.4.22.-) (Metacaspase 2b) (AtMCP2b) (Metacaspase-6) |
| Scaffold_402 | 34092 | G | T | 34 | 1067.18 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_405 | 44526 | C | A | 10 | 321.78 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_414 | 35078 | A | C | 16 | 407.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_417 | 10596 | A | C | 12 | 420.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_423 | 74417 | T | G | 10 | 30.77 | exon | Transversion | 0/1 | Vacuolar cation/proton exchanger 2 (Ca(2+)/H(+) antiporter CAX2) (Ca(2+)/H(+) exchanger 2) (Protein CATION EXCHANGER 2) |
| Scaffold_426 | 34063 | T | A | 142 | 4364.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_428 | 31704 | T | A | 11 | 325.22 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_428 | 31705 | T | G | 24 | 860.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_428 | 53739 | T | A | 133 | 3690.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_428 | 53787 | C | A | 61 | 2029.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_429 | 76726 | C | G | 10 | 321.78 | exon | Transversion | 1/1 | Probable aquaporin TIP3-1 (Tonoplast intrinsic protein 3-1) (OsTIP3;1) |
| Scaffold_432 | 7091 | G | T | 17 | 92.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_440 | 14764 | T | G | 242 | 7694.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_441 | 53121 | T | A | 139 | 4048.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_445 | 32560 | G | T | 13 | 446.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_445 | 62939 | C | G | 14 | 455.77 | exon | Transversion | 1/1 | Unannotated |