| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2009 | 40377 | G | T | 10 | 220.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2397 | 98668 | G | T | 20 | 234.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 1118 | C | G | 10 | 164.78 | CDS | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At2g33760 |
| Scaffold_2398 | 1269 | C | G | 26 | 209.77 | CDS | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At2g33760 |
| Scaffold_2398 | 77524 | A | C | 82 | 1554.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 77539 | T | G | 71 | 67.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 132816 | G | C | 37 | 543.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2400 | 18356 | G | T | 36 | 56.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2400 | 19291 | A | T | 16 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2400 | 19292 | G | C | 16 | 58.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2400 | 72232 | G | T | 15 | 49.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2400 | 72233 | A | C | 14 | 52.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2401 | 57611 | A | C | 250 | 68.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2401 | 57800 | A | C | 250 | 8915.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_2401 | 169904 | G | T | 10 | 67.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2403 | 149678 | A | T | 17 | 40.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2403 | 149679 | A | C | 16 | 52.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2403 | 153771 | C | G | 10 | 32.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2403 | 154266 | T | A | 69 | 135.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2403 | 156115 | G | C | 28 | 964.77 | noncoding | Transversion | 1/1 | Unannotated |