| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1422 | 1086 | A | G | 35 | 340.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1422 | 32875 | C | T | 16 | 58.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1431 | 35931 | A | G | 27 | 302.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1450 | 17330 | G | A | 39 | 105.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1450 | 17519 | G | A | 115 | 1073.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1450 | 17528 | C | T | 98 | 1053.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1456 | 30640 | G | A | 36 | 495.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1456 | 31055 | A | G | 20 | 93.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1456 | 31091 | T | C | 47 | 377.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1456 | 48592 | G | A | 11 | 48.77 | noncoding | Transition | 0/1 | BTB/POZ domain-containing protein At1g30440 |
| Scaffold_1456 | 48593 | C | T | 12 | 105.77 | noncoding | Transition | 0/1 | BTB/POZ domain-containing protein At1g30440 |
| Scaffold_1457 | 43910 | T | C | 12 | 31.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1457 | 43911 | T | C | 12 | 31.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1458 | 4990 | G | A | 11 | 88.77 | noncoding | Transition | 0/1 | Peptide chain release factor PrfB1, chloroplastic (AtPrfB1) (AtPrfB) (Protein HIGH CHLOROPHYLL FLUORESCENCE 109) |
| Scaffold_1459 | 35971 | T | C | 32 | 54.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1473 | 3387 | G | A | 15 | 37.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1476 | 13888 | G | A | 25 | 589.77 | CDS | Transition | 0/1 | Probable phosphoribosylformylglycinamidine synthase, chloroplastic/mitochondrial (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) (Formylglycinamide ribotide amidotransferase) |
| Scaffold_1484 | 43181 | G | A | 19 | 119.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1487 | 8399 | C | T | 64 | 1294.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1499 | 34102 | C | T | 14 | 131.89 | noncoding | Transition | 0/1 | Unannotated |