| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3771 | 1679 | G | C | 239 | 510.77 | noncoding | Transversion | 0/1 | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) (PSI-B) (PsaB) |
| Scaffold_3771 | 1680 | G | T | 239 | 556.77 | noncoding | Transversion | 0/1 | Photosystem I P700 chlorophyll a apoprotein A2 (EC 1.97.1.12) (PSI-B) (PsaB) |
| Scaffold_3771 | 12577 | C | A | 13 | 78.77 | CDS | Transversion | 0/1 | Probable LRR receptor-like serine/threonine-protein kinase At2g16250 (EC 2.7.11.1) |
| Scaffold_3774 | 7239 | T | G | 250 | 182.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3774 | 7285 | A | C | 250 | 407.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3774 | 7286 | A | C | 246 | 712.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3774 | 7315 | A | C | 250 | 33.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3776 | 5063 | C | A | 12 | 278.22 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3781 | 40882 | G | T | 25 | 761.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3786 | 29680 | C | A | 11 | 107.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3787 | 44023 | A | C | 250 | 1668.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3787 | 44024 | G | C | 249 | 750.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3787 | 44036 | A | C | 247 | 1116.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3787 | 44039 | A | C | 248 | 485.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3787 | 44063 | A | C | 249 | 631.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3788 | 45354 | A | C | 250 | 9003.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3788 | 46870 | C | G | 28 | 96.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3788 | 46919 | A | T | 22 | 46.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3789 | 20870 | G | C | 14 | 97.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3789 | 22540 | G | T | 42 | 98.77 | CDS | Transversion | 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] |