| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2977 | 35522 | G | A | 14 | 220.41 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2988 | 43837 | G | A | 49 | 944.77 | CDS | Transition | 0/1 | WAT1-related protein At4g30420 |
| Scaffold_2988 | 43910 | T | C | 52 | 714.77 | CDS | Transition | 0/1 | WAT1-related protein At4g30420 |
| Scaffold_2988 | 43945 | A | G | 35 | 493.77 | CDS | Transition | 0/1 | WAT1-related protein At4g30420 |
| Scaffold_2993 | 23870 | C | T | 16 | 456.98 | noncoding | Transition | 0/1 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) |
| Scaffold_2998 | 38242 | T | C | 16 | 379.78 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2998 | 38308 | G | A | 28 | 287.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2998 | 38314 | A | G | 28 | 434.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3001 | 43619 | T | C | 34 | 83.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g62930, chloroplastic |
| Scaffold_3001 | 43697 | A | G | 29 | 659.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g62930, chloroplastic |
| Scaffold_3001 | 43837 | G | A | 13 | 85.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g62930, chloroplastic |
| Scaffold_3004 | 41044 | C | T | 40 | 565.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3004 | 41088 | G | A | 25 | 372.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3007 | 23682 | C | T | 11 | 93.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3010 | 49642 | A | G | 250 | 625.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3010 | 49705 | T | C | 250 | 318.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3021 | 10714 | T | C | 26 | 202.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3025 | 43975 | A | G | 39 | 646.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3025 | 44818 | G | A | 28 | 269.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 51999 | G | A | 21 | 178.77 | exon | Transition | 0/1 | Unannotated |