| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3894 | 33754 | G | A | 54 | 846.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3898 | 14129 | C | T | 14 | 78.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3898 | 24623 | A | G | 32 | 53.77 | exon | Transition | 0/1 | Beta-amylase 3, chloroplastic (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase) (Beta-amylase 8) (Chloroplast beta-amylase) (CT-BMY) |
| Scaffold_3898 | 46372 | G | A | 83 | 125.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3898 | 46426 | G | A | 120 | 216.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3898 | 46429 | G | A | 120 | 245.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3898 | 46531 | G | A | 82 | 445.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3905 | 43723 | C | T | 21 | 51.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3905 | 43749 | C | T | 19 | 474.89 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3905 | 45033 | G | A | 139 | 1941.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3905 | 45070 | T | C | 192 | 3572.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3905 | 45118 | G | A | 250 | 5583.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3905 | 45194 | G | A | 169 | 1797.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3905 | 45294 | G | A | 32 | 538.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3906 | 16946 | C | T | 250 | 2824.77 | CDS | Transition | 0/1 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (EC 1.6.99.3) (EC 7.1.1.2) (NADH dehydrogenase subunit 7) |
| Scaffold_3906 | 16953 | C | T | 250 | 501.77 | CDS | Transition | 0/1 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (EC 1.6.99.3) (EC 7.1.1.2) (NADH dehydrogenase subunit 7) |
| Scaffold_3906 | 16985 | C | T | 215 | 2228.77 | CDS | Transition | 0/1 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (EC 1.6.99.3) (EC 7.1.1.2) (NADH dehydrogenase subunit 7) |
| Scaffold_3906 | 16991 | C | T | 225 | 2334.77 | CDS | Transition | 0/1 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (EC 1.6.99.3) (EC 7.1.1.2) (NADH dehydrogenase subunit 7) |
| Scaffold_3906 | 17045 | C | T | 250 | 7204.77 | CDS | Transition | 0/1 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (EC 1.6.99.3) (EC 7.1.1.2) (NADH dehydrogenase subunit 7) |
| Scaffold_3906 | 18013 | C | T | 250 | 5295.77 | exon | Transition | 0/1 | Unannotated |