| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3559 | 43542 | A | G | 31 | 78.77 | CDS | Transition | 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_3559 | 43563 | C | T | 31 | 84.77 | CDS | Transition | 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_3562 | 1049 | G | A | 11 | 66.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3566 | 30098 | C | T | 28 | 141.88 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3566 | 44550 | A | G | 250 | 607.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3566 | 44580 | T | C | 250 | 1168.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3566 | 44631 | A | G | 249 | 283.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3566 | 44660 | A | G | 243 | 40.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 12050 | C | T | 196 | 1090.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13115 | C | T | 78 | 911.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13376 | C | T | 230 | 304.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13408 | C | T | 218 | 4535.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13423 | C | T | 158 | 2066.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13438 | C | T | 166 | 459.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13596 | C | T | 75 | 1343.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13733 | C | T | 49 | 675.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13751 | C | T | 44 | 269.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13813 | C | T | 92 | 62.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3572 | 13833 | C | T | 84 | 1099.77 | noncoding | Transition | 0/1 | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) (NADH dehydrogenase subunit 3) |
| Scaffold_3572 | 13889 | C | T | 88 | 428.77 | noncoding | Transition | 0/1 | NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2) (NADH dehydrogenase subunit 3) |