| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2451 | 74259 | C | T | 20 | 69.77 | exon | Transition | 0/1 | Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 homolog (EC 3.1.3.16) (RNA polymerase II-associated protein 2 homolog) |
| Scaffold_2451 | 116963 | A | G | 40 | 680.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2452 | 30040 | C | T | 16 | 33.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2453 | 24858 | T | C | 14 | 55.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2453 | 25181 | A | G | 17 | 86.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2455 | 55997 | G | A | 21 | 43.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2455 | 55998 | A | G | 22 | 46.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2455 | 90557 | A | G | 79 | 2239.77 | CDS | Transition | 1/1 | Unannotated |
| Scaffold_2456 | 113027 | C | T | 164 | 312.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2467 | 69991 | G | A | 10 | 256.84 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2468 | 127408 | T | C | 13 | 52.77 | CDS | Transition | 0/1 | Protein PIR (PIR of plants) (Protein KLUNKER) (AtSRA1) (Protein PIROGI) |
| Scaffold_2475 | 51630 | C | T | 15 | 168.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2475 | 121929 | C | T | 250 | 8821.77 | CDS | Transition | 1/1 | Elongation factor 1-alpha (EF-1-alpha) |
| Scaffold_2475 | 121932 | T | C | 250 | 8739.77 | CDS | Transition | 1/1 | Elongation factor 1-alpha (EF-1-alpha) |
| Scaffold_2475 | 122004 | G | A | 250 | 8941.77 | CDS | Transition | 1/1 | Elongation factor 1-alpha (EF-1-alpha) |
| Scaffold_2475 | 122124 | G | A | 249 | 8204.77 | CDS | Transition | 1/1 | Elongation factor 1-alpha (EF-1-alpha) |
| Scaffold_2475 | 122600 | G | A | 61 | 2004.77 | CDS | Transition | 1/1 | Elongation factor 1-alpha (EF-1-alpha) (Vitronectin-like adhesion protein 1) (PVN1) |
| Scaffold_2478 | 76062 | T | C | 13 | 239.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2479 | 100900 | T | C | 143 | 182.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2479 | 101424 | A | G | 250 | 2625.77 | exon | Transition | 0/1 | Unannotated |