| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3612 | 72446 | C | T | 18 | 94.77 | exon | Transition | 0/1 | Putative cytochrome c biosynthesis ccmC-like mitochondrial protein (ABC transporter I family member 3) (ABC transporter ABCI.3) (AtABCI3) |
| Scaffold_3612 | 72507 | C | T | 24 | 176.77 | exon | Transition | 0/1 | Putative cytochrome c biosynthesis ccmC-like mitochondrial protein (ABC transporter I family member 3) (ABC transporter ABCI.3) (AtABCI3) |
| Scaffold_3612 | 72558 | C | T | 19 | 82.77 | exon | Transition | 0/1 | Putative cytochrome c biosynthesis ccmC-like mitochondrial protein (ABC transporter I family member 3) (ABC transporter ABCI.3) (AtABCI3) |
| Scaffold_3612 | 72660 | C | T | 250 | 7772.77 | exon | Transition | 1/1 | Putative cytochrome c biosynthesis ccmC-like mitochondrial protein (ABC transporter I family member 3) (ABC transporter ABCI.3) (AtABCI3) |
| Scaffold_3612 | 72683 | C | T | 250 | 8979.77 | exon | Transition | 1/1 | Putative cytochrome c biosynthesis ccmC-like mitochondrial protein (ABC transporter I family member 3) (ABC transporter ABCI.3) (AtABCI3) |
| Scaffold_130 | 396135 | A | G | 90 | 44.77 | CDS | Transition | 0/1 | Putative disease resistance protein At4g10780 |
| Scaffold_1940 | 41864 | A | G | 11 | 132.77 | CDS | Transition | 0/1 | Putative disease resistance protein At5g47280 |
| Scaffold_28 | 974638 | T | C | 27 | 53.77 | CDS | Transition | 0/1 | Putative phospholipid-transporting ATPase 9 (AtALA9) (EC 3.6.3.1) (Aminophospholipid flippase 9) |
| Scaffold_3641 | 2739 | A | G | 20 | 447.74 | noncoding | Transition | 0/1 | Putative ribonuclease H protein At1g65750 (EC 3.1.26.4) |
| Scaffold_17 | 13955 | A | G | 29 | 823.77 | exon | Transition | 1/1 | Putative serine/threonine-protein kinase-like protein CCR3 (EC 2.7.11.1) (Protein CRINKLY 4 RELATED 3) (AtCRR3) |
| Scaffold_2939 | 28937 | A | G | 19 | 701.77 | noncoding | Transition | 1/1 | Putative uncharacterized protein ycf15 |
| Scaffold_2939 | 28941 | T | C | 19 | 699.77 | noncoding | Transition | 1/1 | Putative uncharacterized protein ycf15 |
| Scaffold_1790 | 24898 | T | C | 16 | 40.77 | exon | Transition | 0/1 | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) (Pyrophosphate-energized inorganic pyrophosphatase) (H(+)-PPase) (Vacuolar H(+)-pyrophosphatase) |
| Scaffold_901 | 56878 | A | G | 19 | 592.77 | noncoding | Transition | 1/1 | Pyruvate kinase 1, cytosolic (OsPK1) (EC 2.7.1.40) |
| Scaffold_3691 | 51574 | G | A | 30 | 103.77 | CDS | Transition | 0/1 | Pyruvate kinase isozyme A, chloroplastic (EC 2.7.1.40) |
| Scaffold_3691 | 51678 | A | G | 198 | 4073.77 | CDS | Transition | 0/1 | Pyruvate kinase isozyme A, chloroplastic (EC 2.7.1.40) |
| Scaffold_3691 | 51792 | C | T | 149 | 477.77 | CDS | Transition | 0/1 | Pyruvate kinase isozyme A, chloroplastic (EC 2.7.1.40) |
| Scaffold_1625 | 20319 | A | G | 11 | 349.78 | exon | Transition | 1/1 | Receptor-like protein 30 (AtRLP30) |
| Scaffold_519 | 21865 | T | C | 15 | 425.77 | CDS | Transition | 1/1 | Receptor-like protein 38 (AtRLP38) |
| Scaffold_50 | 211157 | A | G | 11 | 299.78 | noncoding | Transition | 1/1 | Receptor-like protein 7 (AtRLP7) |