| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3025 | 45810 | A | G | 31 | 31.77 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3025 | 45833 | C | T | 32 | 104.77 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3025 | 45842 | C | T | 28 | 687.94 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3025 | 45854 | G | A | 24 | 527.77 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 33908 | C | T | 66 | 213.77 | exon | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 33969 | G | A | 52 | 862.77 | exon | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 35063 | G | A | 129 | 1659.77 | CDS | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 35110 | C | T | 131 | 670.77 | CDS | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 35152 | A | G | 99 | 1951.77 | CDS | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 35205 | G | A | 61 | 93.77 | CDS | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_2637 | 61001 | A | G | 19 | 283.77 | CDS | Transition | 0/1 | Cellulose synthase-like protein H1 (EC 2.4.1.-) (OsCslH1) |
| Scaffold_11 | 690130 | G | A | 35 | 319.77 | CDS | Transition | 0/1 | Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1) |
| Scaffold_11 | 690178 | A | G | 32 | 359.77 | CDS | Transition | 0/1 | Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1) |
| Scaffold_11 | 690299 | C | T | 25 | 773.77 | CDS | Transition | 1/1 | Chalcone synthase 1 (EC 2.3.1.74) (Naringenin-chalcone synthase 1) |
| Scaffold_32 | 863551 | A | G | 37 | 704.77 | CDS | Transition | 0/1 | Chaperone protein ClpC, chloroplastic (ATP-dependent Clp protease ATP-binding subunit ClpC homolog) (Casein lytic proteinase C) |
| Scaffold_32 | 863560 | A | G | 40 | 819.77 | CDS | Transition | 0/1 | Chaperone protein ClpC, chloroplastic (ATP-dependent Clp protease ATP-binding subunit ClpC homolog) (Casein lytic proteinase C) |
| Scaffold_32 | 863689 | T | C | 54 | 176.77 | CDS | Transition | 0/1 | Chaperone protein ClpC, chloroplastic (ATP-dependent Clp protease ATP-binding subunit ClpC homolog) (Casein lytic proteinase C) |
| Scaffold_32 | 863698 | T | C | 59 | 359.77 | CDS | Transition | 0/1 | Chaperone protein ClpC, chloroplastic (ATP-dependent Clp protease ATP-binding subunit ClpC homolog) (Casein lytic proteinase C) |
| Scaffold_54 | 215894 | G | A | 22 | 35.77 | CDS | Transition | 0/1 | CHD3-type chromatin-remodeling factor PICKLE (EC 3.6.4.-) (Protein CHROMATIN REMODELING 6) (AtCHR6) (Protein GYMNOS) |
| Scaffold_178 | 553865 | A | G | 250 | 9290.77 | CDS | Transition | 1/1 | Chlorophyll a-b binding protein 3, chloroplastic (LHCII type I CAB-3) (LHCP) |