| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3280 | 15067 | T | C | 250 | 61.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15071 | A | G | 250 | 68.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15074 | T | C | 249 | 127.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15080 | A | G | 250 | 196.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15083 | A | G | 248 | 36.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15087 | T | C | 250 | 428.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15101 | T | C | 250 | 71.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15108 | A | G | 250 | 109.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15110 | A | G | 250 | 260.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3280 | 15118 | T | C | 250 | 314.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3281 | 35145 | G | A | 15 | 49.77 | CDS | Transition | 0/1 | tRNA ligase 1 (AtRLG1) (AtRNL) (AtRlg1p) (EC 6.5.1.3) (Protein AT.I.24-9) |
| Scaffold_3281 | 35146 | A | G | 15 | 46.77 | CDS | Transition | 0/1 | tRNA ligase 1 (AtRLG1) (AtRNL) (AtRlg1p) (EC 6.5.1.3) (Protein AT.I.24-9) |
| Scaffold_3283 | 2911 | G | A | 18 | 296.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3283 | 43427 | C | T | 12 | 36.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3285 | 49072 | C | T | 250 | 1538.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3285 | 49206 | C | T | 127 | 256.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3288 | 6436 | G | A | 242 | 4221.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3289 | 39558 | C | T | 23 | 190.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3290 | 42787 | G | A | 55 | 145.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3290 | 42804 | A | G | 250 | 196.77 | noncoding | Transition | 0/1 | Unannotated |