| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_53 | 1328452 | C | T | 13 | 150.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_53 | 1376391 | T | C | 16 | 83.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_53 | 1804273 | G | A | 12 | 39.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_53 | 1814341 | T | C | 62 | 983.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_54 | 176551 | G | A | 45 | 44.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_54 | 552922 | G | A | 12 | 163.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_54 | 915476 | A | G | 19 | 126.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_54 | 1263494 | T | C | 49 | 117.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_54 | 1381608 | A | G | 12 | 234.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_54 | 1455244 | A | G | 15 | 89.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_54 | 1485133 | A | G | 31 | 31.77 | exon | Transition | 0/1 | Probable LRR receptor-like serine/threonine-protein kinase At1g74360 (EC 2.7.11.1) |
| Scaffold_55 | 198309 | A | G | 21 | 62.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_55 | 199364 | T | C | 18 | 43.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_55 | 200197 | G | A | 13 | 39.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_55 | 233455 | G | A | 12 | 30.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_55 | 267328 | T | C | 10 | 67.77 | CDS | Transition | 0/1 | Ribonuclease III domain-containing protein RNC1, chloroplastic (Chloroplast ribonuclease III domain protein) |
| Scaffold_55 | 286653 | C | T | 87 | 2219.77 | CDS | Transition | 1/1 | Unannotated |
| Scaffold_55 | 843481 | C | T | 11 | 156.78 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_55 | 852809 | C | T | 250 | 3640.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_55 | 853492 | A | G | 17 | 37.77 | CDS | Transition | 0/1 | Unannotated |