| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3602 | 41628 | T | G | 25 | 361.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3603 | 15988 | A | C | 250 | 4171.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3604 | 16226 | T | A | 74 | 74.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3605 | 9309 | A | C | 250 | 234.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3611 | 2567 | T | A | 53 | 1734.77 | intron | Transversion | 1/1 | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3612 | 14521 | C | G | 18 | 55.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3617 | 7789 | C | A | 143 | 36.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3617 | 7795 | T | G | 35 | 132.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3619 | 42111 | G | T | 13 | 36.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3619 | 59689 | G | T | 19 | 606.81 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3620 | 14754 | T | G | 199 | 48.77 | noncoding | Transversion | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 B, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase, subunit 2 B) (NADH-plastoquinone oxidoreductase subunit 2 B) |
| Scaffold_3622 | 4531 | T | G | 13 | 106.77 | noncoding | 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] |
| Scaffold_3622 | 4534 | G | C | 13 | 30.77 | noncoding | 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] |
| Scaffold_3622 | 5225 | C | A | 16 | 52.77 | 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] |
| Scaffold_3622 | 5300 | C | G | 16 | 123.77 | 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] |
| Scaffold_3626 | 59491 | A | T | 16 | 109.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3634 | 19170 | A | T | 17 | 31.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3634 | 25091 | G | T | 17 | 393.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3637 | 5995 | G | T | 201 | 80.77 | noncoding | Transversion | 0/1 | NAD(P)H-quinone oxidoreductase subunit H, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase subunit H) (NADH-plastoquinone oxidoreductase 49 kDa subunit) (NADH-plastoquinone oxidoreductase subunit H) |
| Scaffold_3642 | 20073 | A | C | 10 | 76.77 | CDS | Transversion | 0/1 | Protein Ycf2 |