| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3533 | 16189 | T | C | 250 | 1350.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3533 | 16197 | A | G | 250 | 579.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3533 | 16201 | T | C | 250 | 177.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3536 | 24872 | T | C | 18 | 274.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3536 | 34097 | A | G | 42 | 416.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3538 | 16464 | T | C | 36 | 476.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3540 | 27165 | T | C | 133 | 348.77 | noncoding | Transition | 0/1 | Photosystem II CP47 reaction center protein (PSII 47 kDa protein) (Protein CP-47) |
| Scaffold_3544 | 24367 | A | G | 57 | 218.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3545 | 8501 | G | A | 52 | 1158.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3545 | 8540 | T | C | 249 | 7703.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3545 | 22190 | A | G | 76 | 523.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3545 | 22510 | A | G | 16 | 417.31 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3549 | 11938 | T | C | 52 | 190.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3556 | 5041 | T | C | 17 | 222.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3559 | 42357 | G | A | 25 | 68.77 | 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 | 42372 | C | T | 23 | 413.77 | 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 | 42415 | A | G | 18 | 182.77 | 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 | 42605 | C | T | 17 | 91.77 | 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 | 43165 | C | T | 20 | 103.77 | 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 | 43465 | C | T | 19 | 45.77 | 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] |