| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2405 | 86897 | A | G | 20 | 46.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2406 | 164761 | T | C | 133 | 3595.77 | exon | Transition | 1/1 | Unannotated |
| Scaffold_2407 | 3160 | G | A | 16 | 69.77 | CDS | Transition | 0/1 | Protein PAM68, chloroplastic (PHOTOSYNTHESIS AFFECTED MUTANT 68) |
| Scaffold_2407 | 6890 | G | A | 15 | 399.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2408 | 27853 | C | T | 11 | 76.77 | exon | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28432 | G | A | 29 | 69.77 | CDS | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28536 | C | T | 32 | 311.77 | CDS | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28545 | C | T | 27 | 320.77 | CDS | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28603 | G | A | 15 | 40.77 | CDS | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28729 | A | G | 15 | 226.77 | CDS | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28730 | T | C | 15 | 230.77 | CDS | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 35524 | G | A | 21 | 40.77 | intron | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE1 (Retro element 1) (AtRE1) [Includes: Protease RE1 (EC 3.4.23.-); Reverse transcriptase RE1 (EC 2.7.7.49); Endonuclease RE1] |
| Scaffold_2408 | 98009 | T | C | 12 | 55.77 | exon | Transition | 0/1 | 2-hydroxyisoflavanone synthase (2HI synthase) (EC 1.14.14.87) (CYP Ge-8) (Cytochrome P450 93C2) (Isoflavonoid synthase) |
| Scaffold_2408 | 156916 | A | G | 12 | 333.28 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2408 | 157575 | G | A | 11 | 32.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2408 | 158661 | A | G | 11 | 129.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2408 | 158730 | A | G | 20 | 341.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2409 | 31899 | T | C | 12 | 58.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2412 | 2599 | T | C | 27 | 65.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2417 | 139180 | G | A | 18 | 31.77 | noncoding | Transition | 0/1 | Unannotated |