| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3589 | 16287 | A | G | 22 | 141.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3589 | 17119 | A | G | 31 | 73.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3589 | 17453 | A | G | 13 | 112.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3593 | 65553 | C | T | 15 | 205.77 | exon | Transition | 0/1 | Coumaroyl-CoA:anthocyanidin 3-O-glucoside-6''-O-coumaroyltransferase 1 (EC 2.3.1.-) |
| Scaffold_3600 | 12609 | T | C | 28 | 41.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3600 | 25006 | G | A | 15 | 282.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3600 | 25014 | C | T | 17 | 64.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3600 | 25051 | T | C | 19 | 467.74 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3601 | 16190 | A | G | 69 | 320.77 | exon | Transition | 0/1 | F-box/WD-40 repeat-containing protein At5g21040 |
| Scaffold_3604 | 15481 | G | A | 17 | 308.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3604 | 15506 | G | A | 14 | 223.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3612 | 53776 | A | G | 14 | 36.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3622 | 5267 | C | T | 14 | 136.77 | CDS | 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_3622 | 5268 | G | A | 13 | 130.77 | CDS | 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_3633 | 35428 | T | C | 11 | 247.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3633 | 35429 | T | C | 11 | 245.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3635 | 18085 | G | A | 13 | 38.77 | CDS | Transition | 0/1 | CLIP-associated protein (AtCLASP) |
| Scaffold_3637 | 6061 | C | T | 22 | 552.77 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit H, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit H) (NADH-plastoquinone oxidoreductase 49 kDa subunit) (NADH-plastoquinone oxidoreductase subunit H) |
| Scaffold_3639 | 157 | C | T | 19 | 277.77 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase, subunit 2 A) (NADH-plastoquinone oxidoreductase subunit 2 A) |
| Scaffold_3639 | 166 | C | T | 16 | 195.77 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase, subunit 2 A) (NADH-plastoquinone oxidoreductase subunit 2 A) |