| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2905 | 45359 | T | C | 250 | 971.77 | noncoding | Transition | 0/1 | Photosystem II reaction center protein M (PSII-M) |
| Scaffold_2905 | 45432 | A | G | 250 | 477.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2905 | 45491 | T | C | 248 | 658.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2905 | 45492 | T | C | 248 | 334.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2905 | 45493 | A | G | 250 | 505.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2910 | 21964 | A | G | 17 | 55.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2912 | 68772 | T | C | 15 | 143.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2912 | 68783 | C | T | 15 | 75.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2916 | 3984 | A | G | 13 | 89.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2916 | 13985 | C | T | 17 | 58.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2917 | 48469 | C | T | 50 | 1265.77 | noncoding | Transition | 1/1 | Photosystem II CP47 reaction center protein (PSII 47 kDa protein) (Protein CP-47) |
| Scaffold_2920 | 35608 | G | A | 12 | 104.78 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2921 | 42872 | T | C | 26 | 642.9 | CDS | Transition | 1/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |
| Scaffold_2921 | 42946 | A | G | 12 | 221.77 | CDS | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |
| Scaffold_2922 | 31219 | G | A | 24 | 49.74 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_2922 | 47029 | T | C | 10 | 61.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2922 | 48176 | C | T | 74 | 996.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2923 | 7855 | C | T | 20 | 66.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2928 | 31678 | A | G | 12 | 237.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2929 | 44673 | T | C | 36 | 62.77 | noncoding | Transition | 0/1 | Unannotated |