| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3822 | 1439 | A | G | 15 | 183.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3832 | 31530 | C | T | 16 | 152.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3832 | 31552 | A | G | 12 | 139.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3836 | 26016 | C | T | 19 | 386.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3842 | 4017 | C | T | 10 | 270.53 | noncoding | Transition | 0/1 | Putative AC9 transposase |
| Scaffold_3846 | 50479 | T | C | 250 | 1214.77 | CDS | Transition | 0/1 | Thioredoxin M-type, chloroplastic (Trx-M) |
| Scaffold_3854 | 40090 | G | A | 11 | 243.03 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3854 | 40176 | G | A | 10 | 65.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3855 | 72193 | G | A | 11 | 233.18 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3858 | 20729 | T | C | 244 | 2073.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3860 | 16930 | G | A | 250 | 30.77 | exon | Transition | 0/1 | ATP-dependent zinc metalloprotease FTSH 2, chloroplastic (AtFTSH2) (EC 3.4.24.-) (Protein VARIEGATED 2) |
| Scaffold_3862 | 7584 | A | G | 12 | 73.77 | exon | Transition | 0/1 | SUMO-conjugating enzyme UBC9 (EC 2.3.2.-) (RING-type E3 SUMO transferase UBC9) (UBCAT4B) (Ubiquitin carrier protein 9) (Ubiquitin-conjugating enzyme E2 9) (Ubiquitin-conjugating enzyme E2-17 kDa) (Ubiquitin-protein ligase 9) |
| Scaffold_3862 | 35206 | T | C | 30 | 96.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 35351 | T | C | 138 | 2610.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 35441 | G | A | 201 | 587.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 35456 | T | C | 177 | 563.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 35750 | T | C | 44 | 139.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 35968 | C | T | 83 | 71.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 35989 | G | A | 170 | 758.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |
| Scaffold_3862 | 36025 | G | A | 250 | 1126.77 | CDS | Transition | 0/1 | Eukaryotic translation initiation factor 3 subunit B (eIF3b) (eIF-3-eta) (eIF3 p110) (p82) |