| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2683 | 151962 | C | T | 15 | 352.78 | CDS | Transition | 1/1 | Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic (Chloroplastic RNA splicing factor 1) (Protein CHLOROPLAST RNA SPLICING 1) |
| Scaffold_160 | 15739 | T | C | 71 | 142.77 | CDS | Transition | 0/1 | Clathrin heavy chain 2 |
| Scaffold_160 | 15745 | G | A | 85 | 119.77 | CDS | Transition | 0/1 | Clathrin heavy chain 2 |
| Scaffold_160 | 16985 | C | T | 95 | 3069.77 | CDS | Transition | 1/1 | Clathrin heavy chain 2 |
| Scaffold_2585 | 33506 | A | G | 13 | 378.77 | CDS | Transition | 1/1 | CLP protease regulatory subunit CLPX3, mitochondrial |
| Scaffold_2406 | 61110 | A | G | 25 | 695.77 | CDS | Transition | 0/1 | Coatomer subunit beta'-3 (Beta'-coat protein 3) (Beta'-COP 3) |
| Scaffold_2406 | 61149 | C | T | 21 | 637.77 | CDS | Transition | 0/1 | Coatomer subunit beta'-3 (Beta'-coat protein 3) (Beta'-COP 3) |
| Scaffold_3326 | 12441 | G | A | 72 | 41.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12466 | A | G | 113 | 626.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12528 | C | T | 147 | 1193.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12613 | T | C | 58 | 721.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12727 | T | C | 38 | 298.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12781 | A | G | 37 | 363.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12841 | C | T | 30 | 407.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12861 | T | C | 25 | 246.77 | CDS | Transition | 0/1 | COP1-interactive protein 1 |
| Scaffold_1052 | 50831 | A | G | 12 | 129.77 | noncoding | Transition | 0/1 | Cyclase-like protein 2 (OsCYL2) |
| Scaffold_435 | 5819 | C | T | 17 | 378.77 | CDS | Transition | 1/1 | Cystathionine beta-lyase, chloroplastic (CBL) (EC 4.4.1.8) (Beta-cystathionase) (Cysteine lyase) |
| Scaffold_451 | 69053 | G | A | 10 | 169.77 | intron | Transition | 0/1 | Cysteine proteinase RD21A (EC 3.4.22.-) (Protein RESPONSIVE TO DEHYDRATION 21) (RD21) |
| Scaffold_3109 | 20 | C | T | 66 | 1627.77 | intron | Transition | 0/1 | Cytochrome b (Complex III subunit 3) (Complex III subunit III) (Cytochrome b-c1 complex subunit 3) (Ubiquinol-cytochrome-c reductase complex cytochrome b subunit) |
| Scaffold_3109 | 86 | C | T | 250 | 974.77 | intron | Transition | 0/1 | Cytochrome b (Complex III subunit 3) (Complex III subunit III) (Cytochrome b-c1 complex subunit 3) (Ubiquinol-cytochrome-c reductase complex cytochrome b subunit) |