| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2 | 702676 | C | T | 10 | 30.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2 | 847805 | A | G | 12 | 85.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2 | 1099364 | G | A | 19 | 363.77 | exon | Transition | 0/1 | Probably inactive leucine-rich repeat receptor-like protein kinase At2g25790 |
| Scaffold_2 | 1099488 | G | A | 20 | 469.77 | exon | Transition | 0/1 | LRR receptor-like serine/threonine-protein kinase (EC 2.7.11.1) (LRR receptor-like serine/threonine-protein kinase At4g26540) (Protein RECEPTOR OF RGF1) (Protein RGF1 INSENSITIVE 3) |
| Scaffold_2 | 1128622 | T | C | 36 | 45.77 | CDS | Transition | 0/1 | Receptor-like protein 53 (AtRLP53) |
| Scaffold_2 | 1361786 | A | G | 10 | 58.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2 | 1554923 | C | T | 19 | 69.77 | exon | Transition | 0/1 | Tripeptidyl-peptidase 2 (EC 3.4.14.10) (Tripeptidyl-peptidase II) (TPPII) |
| Scaffold_2 | 1554972 | A | G | 18 | 46.77 | exon | Transition | 0/1 | Tripeptidyl-peptidase 2 (EC 3.4.14.10) (Tripeptidyl-peptidase II) (TPPII) |
| Scaffold_2 | 1576051 | C | T | 244 | 360.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2 | 1602837 | A | C,T | 11 | 415.77 | intron | Transition | 1/2 | Unannotated |
| Scaffold_2 | 1604654 | G | A | 26 | 451.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2 | 1681392 | C | T | 53 | 365.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2113543 | C | T | 20 | 30.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2169013 | C | T | 13 | 55.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2302711 | A | G | 14 | 36.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2428097 | C | T | 13 | 39.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2447843 | T | C | 19 | 37.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2584104 | C | T | 13 | 286.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2 | 2708764 | A | G | 10 | 171.78 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g32415, mitochondrial |
| Scaffold_4 | 243953 | G | A | 11 | 61.77 | CDS | Transition | 0/1 | Unannotated |