| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1104 | 50836 | A | C | 21 | 751.77 | noncoding | Transversion | 1/1 | E3 ubiquitin-protein ligase RDUF1 (EC 2.3.2.27) (RING and DUF1117 domain-containing protein 1) (AtRDUF1) (RING-type E3 ubiquitin transferase RDUF1) |
| Scaffold_1104 | 50837 | G | T | 23 | 831.77 | noncoding | Transversion | 1/1 | E3 ubiquitin-protein ligase RDUF1 (EC 2.3.2.27) (RING and DUF1117 domain-containing protein 1) (AtRDUF1) (RING-type E3 ubiquitin transferase RDUF1) |
| Scaffold_1117 | 15724 | G | T | 93 | 1788.77 | noncoding | Transversion | 0/1 | 60S ribosomal protein L7-2 |
| Scaffold_1117 | 15775 | T | A | 76 | 147.77 | noncoding | Transversion | 0/1 | 60S ribosomal protein L7-2 |
| Scaffold_1118 | 19129 | G | T | 10 | 266.8 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_1118 | 49340 | G | T | 16 | 479.77 | CDS | Transversion | 1/1 | APO protein 3, mitochondrial |
| Scaffold_1119 | 22809 | T | A | 12 | 439.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1126 | 46559 | A | T | 14 | 137.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1126 | 55596 | G | T | 116 | 3523.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_1148 | 37470 | G | C | 64 | 136.77 | CDS | Transversion | 0/1 | Mitochondrial adenine nucleotide transporter ADNT1 (Adenine nucleotide transporter 1) |
| Scaffold_1152 | 33577 | A | T | 11 | 370.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1153 | 51299 | A | T | 35 | 1149.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1153 | 52943 | A | C | 175 | 6787.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_1159 | 38909 | C | A | 14 | 395.77 | exon | Transversion | 1/1 | Probable disease resistance protein At4g27220 |
| Scaffold_1180 | 19161 | T | A | 15 | 61.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1180 | 19179 | G | C | 14 | 60.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1180 | 52408 | A | T | 11 | 399.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1182 | 49520 | C | A | 14 | 463.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_1187 | 31615 | A | C | 10 | 169.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1194 | 15449 | G | T | 116 | 3109.77 | exon | Transversion | 1/1 | Subtilisin-like protease SBT1.4 (EC 3.4.21.-) (Subtilase subfamily 1 member 4) (AtSBT1.4) |