| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3180 | 33336 | A | C | 250 | 40.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 33338 | G | C | 250 | 93.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3187 | 18249 | T | A | 69 | 454.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3192 | 77 | A | T | 250 | 355.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3196 | 12827 | T | G | 97 | 261.82 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3200 | 7782 | T | G | 25 | 567.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3203 | 28062 | C | A | 27 | 83.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3203 | 28127 | T | A | 11 | 76.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3203 | 28128 | T | A | 11 | 76.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20357 | A | C | 250 | 426.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20371 | G | T | 250 | 1436.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3221 | 36318 | C | A | 28 | 79.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3221 | 36346 | A | T | 14 | 264.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3221 | 36347 | G | T | 14 | 258.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3244 | 18148 | A | T | 73 | 109.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3244 | 18253 | A | C | 250 | 114.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3257 | 30704 | C | G | 20 | 179.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3259 | 15885 | A | T | 25 | 543.77 | CDS | Transversion | 0/1 | 7-deoxyloganetin glucosyltransferase (EC 2.4.1.324) (Genipin glucosyltransferase) (UDP-glucose glucosyltransferase 2) (GjUGT2) (UDP-glycosyltransferase 85A24) |
| Scaffold_3259 | 15961 | C | A | 82 | 2023.77 | CDS | Transversion | 0/1 | 7-deoxyloganetin glucosyltransferase (EC 2.4.1.324) (Genipin glucosyltransferase) (UDP-glucose glucosyltransferase 2) (GjUGT2) (UDP-glycosyltransferase 85A24) |
| Scaffold_3266 | 21158 | T | G | 39 | 142.77 | exon | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At1g71460, chloroplastic |