| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_16 | 1256707 | C | T | 10 | 346.78 | exon | Transition | 1/1 | Berberine bridge enzyme-like 13 (AtBBE-like 13) (EC 1.1.1.194) (EC 1.1.1.195) |
| Scaffold_57 | 1338026 | G | A | 13 | 364.22 | intron | Transition | 0/1 | Beta-galactosidase 1 (Lactase 1) (EC 3.2.1.23) |
| Scaffold_57 | 1339462 | T | C | 30 | 801.77 | CDS | Transition | 0/1 | Beta-galactosidase 1 (Lactase 1) (EC 3.2.1.23) |
| Scaffold_148 | 151349 | A | G | 23 | 700.77 | intron | Transition | 1/1 | Beta-glucosidase 44 (AtBGLU44) (EC 3.2.1.21) |
| Scaffold_296 | 22254 | G | A | 112 | 2595.77 | noncoding | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 22335 | T | C | 81 | 65.77 | noncoding | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 24653 | G | A | 140 | 31.77 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 24784 | G | A | 93 | 1872.77 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 24787 | C | T | 95 | 1903.77 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 25054 | T | C | 46 | 81.77 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 25072 | T | C | 46 | 112.77 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 25318 | T | C | 28 | 838.96 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_741 | 7525 | G | A | 27 | 919.77 | CDS | Transition | 1/1 | BTB/POZ domain-containing protein At5g66560 |
| Scaffold_741 | 8508 | C | T | 17 | 574.77 | CDS | Transition | 1/1 | BTB/POZ domain-containing protein At5g66560 |
| Scaffold_173 | 567053 | A | G | 24 | 723.77 | CDS | Transition | 1/1 | Calcium-dependent protein kinase (CDPK) (EC 2.7.11.1) |
| Scaffold_181 | 425670 | G | A | 54 | 1677.77 | CDS | Transition | 0/1 | Calcium-dependent protein kinase 1 (OsCDPK1) (OsCPK1) (EC 2.7.11.1) |
| Scaffold_41 | 925305 | T | C | 10 | 256.8 | CDS | Transition | 1/1 | Calcium-dependent protein kinase 11 (EC 2.7.11.1) (Calcium-dependent protein kinase isoform CDPK2) (AtCDPK2) |
| Scaffold_58 | 737152 | A | G | 12 | 49.77 | CDS | Transition | 0/1 | Calmodulin-binding transcription activator 4 (AtCAMTA4) (AtFIN21) (Ethylene-induced calmodulin-binding protein 4) (EICBP4) (Ethylene-induced calmodulin-binding protein d) (EICBP.d) (Signal-responsive protein 5) (AtSR5) |
| Scaffold_51 | 428396 | T | C | 19 | 564.88 | intron | Transition | 0/1 | Calnexin homolog |
| Scaffold_523 | 49264 | G | A | 234 | 8063.77 | CDS | Transition | 1/1 | Calnexin homolog |