| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_632 | 8663 | C | A | 44 | 183.77 | exon | Transversion | 0/1 | Protein JINGUBANG |
| Scaffold_632 | 59488 | A | T | 62 | 210.77 | noncoding | Transversion | 0/1 | Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (EC 2.4.99.18) (Ribophorin II) (RPN-II) (Ribophorin-2) |
| Scaffold_634 | 61590 | T | G | 205 | 1915.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_636 | 3732 | G | T | 11 | 193.22 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_637 | 31723 | T | G | 27 | 159.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_647 | 42508 | G | C | 32 | 317.77 | intron | Transversion | 0/1 | Patatin-like protein 2 (AtPLP2) (EC 3.1.1.-) (Patatin-related phospholipase A IIalpha) (pPLAIIa) (Phospholipase A IIA) (AtPLAIIA) |
| Scaffold_654 | 23818 | G | C | 10 | 143.77 | exon | Transversion | 0/1 | Probable LRR receptor-like serine/threonine-protein kinase At3g47570 (EC 2.7.11.1) |
| Scaffold_654 | 49590 | T | G | 13 | 122.78 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_655 | 19419 | T | G | 46 | 109.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_657 | 27230 | A | T | 16 | 43.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_658 | 5377 | A | T | 11 | 211.31 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_662 | 60040 | A | C | 11 | 123.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_663 | 63842 | C | G | 10 | 32.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_664 | 20154 | C | A | 25 | 145.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_664 | 20379 | A | C | 24 | 279.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_666 | 42236 | C | A | 24 | 249.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_669 | 43810 | T | G | 248 | 1998.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_669 | 43840 | G | T | 245 | 3426.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_669 | 44182 | C | A | 108 | 2360.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_669 | 45842 | T | A | 63 | 1374.77 | CDS | Transversion | 0/1 | 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (HMG-CoA reductase 1) (EC 1.1.1.34) |