| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2811 | 9435 | C | T | 22 | 202.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2811 | 9603 | A | G | 73 | 1290.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2812 | 59112 | C | T | 25 | 658.79 | exon | 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_2815 | 5197 | G | A | 99 | 2049.77 | exon | Transition | 0/1 | Probable inactive dual specificity protein phosphatase-like At4g18593 |
| Scaffold_2815 | 5389 | C | T | 24 | 544.77 | CDS | Transition | 0/1 | Probable inactive dual specificity protein phosphatase-like At4g18593 |
| Scaffold_2831 | 9469 | G | A | 116 | 3874.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_2839 | 7192 | A | G | 39 | 70.78 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2839 | 17707 | A | C,T | 14 | 1068.77 | noncoding | Transition | 1/2 | Unannotated |
| Scaffold_2839 | 17708 | G | A | 67 | 1138.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2839 | 22134 | G | A | 51 | 110.79 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2840 | 10724 | T | C | 11 | 36.77 | CDS | Transition | 0/1 | Acetolactate synthase small subunit 1, chloroplastic (Acetohydroxy-acid synthase small subunit) (AHAS) (ALS) (Protein valine-tolerant 1) |
| Scaffold_2841 | 101 | C | T | 133 | 4890.77 | intron | Transition | 1/1 | Unannotated |
| Scaffold_2849 | 6856 | G | A | 13 | 203.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2849 | 6898 | A | G | 29 | 295.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2849 | 6943 | A | G | 46 | 673.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2849 | 6975 | G | A | 33 | 546.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2849 | 47774 | A | G | 12 | 249.84 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2849 | 47800 | A | G | 12 | 250.88 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2852 | 4408 | T | C | 24 | 635.79 | exon | Transition | 0/1 | Amino acid permease 3 (Amino acid transporter AAP3) |
| Scaffold_2852 | 4510 | C | T | 25 | 705.94 | exon | Transition | 0/1 | Amino acid permease 3 (Amino acid transporter AAP3) |