| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3243 | 72820 | A | T | 15 | 70.77 | exon | Transversion | 0/1 | Mediator of RNA polymerase II transcription subunit 13 (Protein GRAND CENTRAL) (Protein MACCHI-BOU 2) |
| Scaffold_3244 | 18234 | A | C | 250 | 605.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3244 | 18305 | G | T | 250 | 49.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3244 | 18359 | T | G | 32 | 1125.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3244 | 44562 | T | G | 12 | 383.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3245 | 33307 | A | T | 250 | 94.77 | noncoding | Transversion | 0/1 | Photosystem II protein D1 (PSII D1 protein) (EC 1.10.3.9) (Photosystem II Q(B) protein) |
| Scaffold_3245 | 33528 | C | G | 26 | 544.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3249 | 43720 | G | C | 30 | 919.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3251 | 53260 | C | A | 112 | 153.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3252 | 18871 | A | C | 144 | 133.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3253 | 26944 | A | C | 39 | 1313.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3253 | 26945 | A | C | 36 | 1226.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3253 | 41774 | T | A | 21 | 176.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_3253 | 41852 | A | C | 19 | 180.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_3253 | 41887 | C | A | 29 | 342.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_3253 | 41970 | C | A | 19 | 223.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_3259 | 15630 | C | A | 13 | 361.28 | 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 | 10 | 343.78 | CDS | Transversion | 1/1 | 7-deoxyloganetin glucosyltransferase (EC 2.4.1.324) (Genipin glucosyltransferase) (UDP-glucose glucosyltransferase 2) (GjUGT2) (UDP-glycosyltransferase 85A24) |
| Scaffold_3266 | 21158 | T | G | 15 | 466.77 | exon | Transversion | 1/1 | Pentatricopeptide repeat-containing protein At1g71460, chloroplastic |
| Scaffold_3269 | 42506 | T | A | 17 | 293.77 | noncoding | Transversion | 0/1 | Unannotated |