| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_122 | 323090 | A | T | 14 | 33.77 | intron | Transversion | 0/1 | GDP-L-galactose phosphorylase 1 (EC 2.7.7.69) (Protein VITAMIN C DEFECTIVE 2) |
| Scaffold_123 | 464978 | G | T | 39 | 50.77 | noncoding | Transversion | 0/1 | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 3, chloroplastic (EC 2.1.1.14) (Cobalamin-independent methionine synthase 3) (AtMS3) |
| Scaffold_123 | 464980 | A | T | 50 | 121.77 | noncoding | Transversion | 0/1 | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 3, chloroplastic (EC 2.1.1.14) (Cobalamin-independent methionine synthase 3) (AtMS3) |
| Scaffold_123 | 469331 | T | G | 27 | 31.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_124 | 293454 | G | T | 30 | 41.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_125 | 77230 | T | A | 31 | 106.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_125 | 79169 | T | A | 20 | 634.81 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_125 | 79171 | G | C | 18 | 560.94 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_125 | 197923 | G | T | 19 | 40.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_125 | 197924 | A | C | 22 | 74.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_125 | 198028 | C | G | 78 | 77.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_126 | 60641 | C | A | 36 | 35.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_126 | 195837 | T | A | 27 | 197.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_126 | 195838 | G | T | 26 | 200.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_126 | 407754 | G | C | 18 | 533.1 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_127 | 12154 | A | T | 18 | 73.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_127 | 12253 | T | G | 15 | 46.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_127 | 12254 | C | A | 15 | 46.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_127 | 153608 | A | T | 24 | 224.77 | CDS | Transversion | 0/1 | Indole-3-acetaldehyde oxidase (IAA oxidase) (EC 1.2.3.7) (Aldehyde oxidase 1) (AO-1) (AtAO-1) (AtAO1) |
| Scaffold_127 | 463851 | T | A | 38 | 53.77 | noncoding | Transversion | 0/1 | Unannotated |