| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_690 | 62625 | C | A | 13 | 139.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_691 | 26659 | T | G | 10 | 230.22 | intron | Transversion | 0/1 | Aluminum-activated malate transporter 9 (AtALMT9) |
| Scaffold_693 | 25778 | T | G | 13 | 42.77 | intron | Transversion | 0/1 | Branched-chain amino acid aminotransferase 2, chloroplastic (HlBCAT2) (EC 2.6.1.42) |
| Scaffold_693 | 25779 | T | G | 13 | 66.77 | intron | Transversion | 0/1 | Branched-chain amino acid aminotransferase 2, chloroplastic (HlBCAT2) (EC 2.6.1.42) |
| Scaffold_694 | 2343 | T | A | 42 | 70.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_716 | 22693 | A | T | 23 | 140.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_717 | 7038 | G | C | 24 | 480.77 | noncoding | Transversion | 0/1 | Spermidine synthase (SPDSY) (EC 2.5.1.16) (Putrescine aminopropyltransferase) |
| Scaffold_724 | 3615 | G | C | 13 | 317.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_726 | 62567 | C | G | 24 | 223.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_728 | 25485 | G | T | 36 | 52.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_730 | 60811 | C | A | 17 | 103.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_733 | 3629 | C | G | 11 | 92.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_733 | 54002 | T | A | 11 | 128.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_733 | 55697 | A | T | 33 | 730.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_733 | 55698 | C | G | 30 | 521.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_735 | 25633 | A | T | 10 | 51.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_738 | 4137 | A | C | 11 | 120.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_739 | 65433 | T | G | 14 | 196.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_741 | 7773 | G | C | 19 | 134.77 | CDS | Transversion | 0/1 | BTB/POZ domain-containing protein At5g66560 |
| Scaffold_741 | 42535 | A | T | 33 | 192.77 | intron | Transversion | 0/1 | Unannotated |