| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1078 | 25929 | C | T | 76 | 598.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1080 | 825 | A | G | 91 | 2035.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1080 | 1319 | G | A | 76 | 1840.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1081 | 386 | T | C | 61 | 880.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1081 | 1337 | T | C | 43 | 799.77 | exon | Transition | 0/1 | Peptidyl-prolyl cis-trans isomerase CYP20-1 (PPIase CYP20-1) (EC 5.2.1.8) (Cyclophilin of 20 kDa 1) (Rotamase CYP20-1) (Rotamase cyclophilin-7) |
| Scaffold_1081 | 1338 | G | A | 56 | 1110.77 | exon | Transition | 0/1 | Peptidyl-prolyl cis-trans isomerase CYP20-1 (PPIase CYP20-1) (EC 5.2.1.8) (Cyclophilin of 20 kDa 1) (Rotamase CYP20-1) (Rotamase cyclophilin-7) |
| Scaffold_1081 | 1435 | G | A | 24 | 241.77 | exon | Transition | 0/1 | Peptidyl-prolyl cis-trans isomerase CYP22 (PPIase CYP22) (EC 5.2.1.8) (Cyclophilin of 22 kDa) (Cyclophilin-22) |
| Scaffold_1084 | 55819 | T | C | 22 | 134.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1084 | 55822 | G | A | 25 | 229.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1088 | 10019 | T | C | 21 | 118.77 | noncoding | Transition | 0/1 | Nudix hydrolase 8 (AtNUDT8) (EC 3.6.1.-) |
| Scaffold_1088 | 10020 | A | G | 22 | 139.77 | noncoding | Transition | 0/1 | Nudix hydrolase 8 (AtNUDT8) (EC 3.6.1.-) |
| Scaffold_1089 | 56845 | T | C | 64 | 210.77 | exon | Transition | 0/1 | TMV resistance protein N |
| Scaffold_1099 | 18682 | C | T | 13 | 113.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1104 | 16698 | A | G | 14 | 125.94 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1105 | 16540 | A | G | 13 | 121.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1109 | 8705 | A | G | 12 | 171.77 | noncoding | Transition | 0/1 | Protein Asterix |
| Scaffold_1113 | 18369 | A | G,T | 31 | 1707.77 | noncoding | Transition | 1/2 | Unannotated |
| Scaffold_1113 | 18370 | G | A | 74 | 914.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1114 | 50874 | A | G | 20 | 67.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1117 | 15649 | A | G | 139 | 265.77 | noncoding | Transition | 0/1 | 60S ribosomal protein L7-2 |