| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_296 | 25288 | A | C | 30 | 808.78 | exon | Transversion | 1/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 68874 | T | A | 42 | 227.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_306 | 66246 | T | A | 19 | 89.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_306 | 66247 | T | G | 18 | 52.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_309 | 81717 | A | C | 24 | 59.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_312 | 15500 | T | A | 16 | 335.77 | exon | Transversion | 0/1 | EID1-like F-box protein 2 |
| Scaffold_314 | 66694 | C | G | 10 | 124.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_319 | 56707 | C | A | 15 | 445.96 | CDS | Transversion | 1/1 | 50S ribosomal protein L27, chloroplastic (CL27) |
| Scaffold_319 | 58659 | T | A | 60 | 36.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_320 | 14646 | T | G | 12 | 166.77 | exon | Transversion | 0/1 | Probable inactive histone-lysine N-methyltransferase SUVR2 (Protein SET DOMAIN GROUP 18) (Suppressor of variegation 3-9-related protein 2) (Su(var)3-9-related protein 2) |
| Scaffold_325 | 27411 | A | T | 10 | 144.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_327 | 44564 | A | C | 13 | 110.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_327 | 50556 | A | C | 18 | 40.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_329 | 45252 | C | G | 26 | 40.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_329 | 66409 | T | G | 11 | 124.77 | intron | Transversion | 0/1 | Putative calcium-transporting ATPase 11, plasma membrane-type (EC 7.2.2.10) (Ca(2+)-ATPase isoform 11) |
| Scaffold_335 | 9142 | G | T | 27 | 747.79 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_335 | 52647 | A | T | 13 | 73.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_336 | 56370 | C | G | 14 | 43.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_343 | 65268 | T | G | 16 | 278.9 | CDS | Transversion | 0/1 | 3-dehydroquinate synthase, chloroplastic (EC 4.2.3.4) |
| Scaffold_343 | 79740 | G | T | 11 | 155.77 | noncoding | Transversion | 0/1 | Unannotated |