| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_46 | 117851 | A | C | 10 | 61.77 | intron | Transversion | 0/1 | Sodium/calcium exchanger NCL (Na(+)/Ca(2+)-exchange protein NCL) (Protein NCX-like) (AtNCL) |
| Scaffold_46 | 117852 | G | T | 12 | 55.77 | intron | Transversion | 0/1 | Sodium/calcium exchanger NCL (Na(+)/Ca(2+)-exchange protein NCL) (Protein NCX-like) (AtNCL) |
| Scaffold_46 | 517076 | C | A | 11 | 275.56 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 542505 | T | A | 17 | 61.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 542506 | T | G | 17 | 58.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 570046 | T | A | 64 | 107.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 665449 | G | C | 22 | 37.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 889670 | T | G | 17 | 49.77 | exon | Transversion | 0/1 | L-type lectin-domain containing receptor kinase S.4 (LecRK-S.4) (EC 2.7.11.1) |
| Scaffold_46 | 1075323 | C | A | 15 | 98.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1093493 | C | A | 21 | 242.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1097444 | T | A | 25 | 76.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1106560 | T | A | 25 | 34.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1167601 | T | A | 26 | 34.77 | exon | Transversion | 0/1 | L-type lectin-domain containing receptor kinase S.4 (LecRK-S.4) (EC 2.7.11.1) |
| Scaffold_46 | 1509811 | T | A | 35 | 512.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1509858 | A | T | 33 | 50.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1788272 | A | C | 36 | 45.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1788872 | A | C | 19 | 49.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 156846 | A | C | 23 | 53.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 244186 | T | A | 33 | 1083.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_47 | 244189 | A | T | 77 | 2797.77 | intron | Transversion | 1/1 | Unannotated |