| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3243 | 73332 | C | T | 59 | 488.77 | exon | Transition | 0/1 | Mediator of RNA polymerase II transcription subunit 13 (Protein GRAND CENTRAL) (Protein MACCHI-BOU 2) |
| Scaffold_3243 | 73468 | C | T | 63 | 35.77 | exon | Transition | 0/1 | Mediator of RNA polymerase II transcription subunit 13 (Protein GRAND CENTRAL) (Protein MACCHI-BOU 2) |
| Scaffold_3244 | 18348 | A | G | 23 | 529.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18492 | C | T | 19 | 47.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3257 | 30693 | G | A | 20 | 206.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3257 | 30698 | C | T | 20 | 249.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3259 | 15853 | T | C | 31 | 654.77 | CDS | Transition | 0/1 | 7-deoxyloganetin glucosyltransferase (EC 2.4.1.324) (Genipin glucosyltransferase) (UDP-glucose glucosyltransferase 2) (GjUGT2) (UDP-glycosyltransferase 85A24) |
| Scaffold_3259 | 15854 | A | G | 28 | 592.77 | CDS | Transition | 0/1 | 7-deoxyloganetin glucosyltransferase (EC 2.4.1.324) (Genipin glucosyltransferase) (UDP-glucose glucosyltransferase 2) (GjUGT2) (UDP-glycosyltransferase 85A24) |
| Scaffold_3259 | 15877 | G | A | 22 | 431.77 | CDS | Transition | 0/1 | 7-deoxyloganetin glucosyltransferase (EC 2.4.1.324) (Genipin glucosyltransferase) (UDP-glucose glucosyltransferase 2) (GjUGT2) (UDP-glycosyltransferase 85A24) |
| Scaffold_3260 | 13458 | C | T | 14 | 262.9 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 B, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase, subunit 2 B) (NADH-plastoquinone oxidoreductase subunit 2 B) |
| Scaffold_3267 | 12786 | A | G | 12 | 227.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3268 | 36794 | C | T | 27 | 399.77 | exon | Transition | 0/1 | Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II) |
| Scaffold_3273 | 3469 | T | C | 35 | 58.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 46035 | T | C | 13 | 153.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 46412 | C | T | 10 | 44.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 46445 | A | G | 10 | 196.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 56780 | G | A | 231 | 776.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 56798 | G | A | 169 | 2341.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 56809 | T | C | 142 | 2822.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3274 | 56944 | A | G | 126 | 1044.77 | CDS | Transition | 0/1 | Unannotated |