| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2404 | 101395 | G | T | 144 | 625.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2404 | 156711 | A | C | 18 | 49.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2404 | 169239 | A | C | 14 | 86.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2405 | 86558 | C | G | 13 | 39.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2406 | 158067 | A | C | 36 | 47.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2407 | 6946 | C | A | 27 | 614.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2408 | 27850 | T | A | 11 | 73.77 | exon | Transversion | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28469 | T | G | 31 | 74.77 | CDS | Transversion | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28623 | A | T | 15 | 42.77 | CDS | Transversion | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28656 | G | T | 19 | 60.77 | CDS | Transversion | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 28899 | T | A | 26 | 431.77 | CDS | Transversion | 0/1 | Mitogen-activated protein kinase kinase kinase YODA (EC 2.7.11.25) (YODA MAPKK kinase) |
| Scaffold_2408 | 35526 | C | A | 21 | 40.77 | intron | Transversion | 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 | 98010 | G | T | 13 | 49.77 | exon | Transversion | 0/1 | 2-hydroxyisoflavanone synthase (2HI synthase) (EC 1.14.14.87) (CYP Ge-8) (Cytochrome P450 93C2) (Isoflavonoid synthase) |
| Scaffold_2408 | 158684 | G | T | 12 | 51.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2408 | 158700 | G | C | 15 | 199.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2408 | 158737 | T | A | 17 | 68.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2409 | 31895 | T | A | 11 | 61.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2409 | 34905 | C | A | 20 | 31.77 | CDS | Transversion | 0/1 | Probable manganese-transporting ATPase PDR2 (EC 3.6.3.-) (Protein MALE GAMETOGENESIS IMPAIRED ANTHERS) (Protein PHOSPHATE DEFICIENCY RESPONSE 2) |
| Scaffold_2409 | 80563 | C | A | 20 | 102.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2409 | 105989 | C | G | 12 | 67.77 | exon | Transversion | 0/1 | Unannotated |