| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_40 | 207305 | C | A | 242 | 932.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 276411 | T | G | 19 | 76.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 431794 | C | A | 55 | 1385.77 | CDS | Transversion | 0/1 | Probable methyltransferase PMT3 (EC 2.1.1.-) |
| Scaffold_40 | 433635 | G | C | 20 | 147.77 | intron | Transversion | 0/1 | Probable methyltransferase PMT25 (EC 2.1.1.-) |
| Scaffold_40 | 681581 | T | A | 13 | 43.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 817337 | C | A | 10 | 216.1 | exon | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At5g56310 |
| Scaffold_40 | 1267005 | A | T | 24 | 414.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1268829 | G | T | 18 | 84.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1270146 | A | T | 11 | 65.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1270401 | G | T | 13 | 146.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1271097 | C | A | 162 | 1663.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1331009 | G | C | 34 | 451.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1372023 | G | T | 21 | 473.82 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1376476 | G | T | 12 | 56.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1524493 | A | T | 11 | 33.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_40 | 1617556 | T | A | 10 | 150.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_41 | 151198 | T | A | 17 | 168.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_41 | 151456 | A | T | 70 | 939.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_41 | 295227 | T | A | 15 | 291.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_41 | 314762 | C | A | 23 | 95.77 | CDS | Transversion | 0/1 | Unannotated |