| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_4000 | 43984 | A | G | 22 | 187.77 | noncoding | Transition | 0/1 | noncoding |
| Scaffold_4005 | 48204 | T | C | 249 | 500.77 | noncoding | Transition | 0/1 | noncoding |
| Scaffold_4005 | 48219 | A | G | 248 | 62.77 | noncoding | Transition | 0/1 | noncoding |
| Scaffold_4005 | 48220 | T | C | 249 | 107.77 | noncoding | Transition | 0/1 | noncoding |
| Scaffold_4006 | 4324 | A | G | 24 | 63.77 | CDS | Transition | 0/1 | noncoding |
| Scaffold_4006 | 4345 | C | T | 26 | 132.77 | CDS | Transition | 0/1 | noncoding |
| Scaffold_4006 | 4400 | C | T | 13 | 146.77 | CDS | Transition | 0/1 | noncoding |
| Scaffold_4006 | 4429 | T | C | 10 | 82.77 | CDS | Transition | 0/1 | noncoding |
| Scaffold_4006 | 4739 | C | T | 10 | 97.77 | CDS | Transition | 0/1 | noncoding |
| Scaffold_4007 | 22932 | T | C | 102 | 172.77 | noncoding | Transition | 0/1 | noncoding |
| Scaffold_4007 | 31544 | G | A | 250 | 7994.77 | noncoding | Transition | 1/1 | noncoding |
| Scaffold_4007 | 31652 | A | G | 248 | 9514.77 | noncoding | Transition | 1/1 | noncoding |
| Scaffold_4007 | 31707 | T | C | 53 | 1688.77 | noncoding | Transition | 1/1 | noncoding |
| Scaffold_4007 | 31715 | A | G | 34 | 1144.77 | noncoding | Transition | 1/1 | noncoding |
| Scaffold_4010 | 21197 | A | G | 115 | 49.74 | noncoding | Transition | 1/1 | noncoding |
| Scaffold_4013 | 3216 | C | T | 10 | 45.77 | exon | Transition | 0/1 | noncoding |
| Scaffold_4013 | 22370 | G | A | 16 | 535.77 | noncoding | Transition | 1/1 | noncoding |
| Scaffold_165 | 557230 | T | C | 31 | 441.77 | CDS | Transition | 0/1 | N-terminal acetyltransferase A complex auxiliary subunit NAA15 (AtNAA15) (Protein OMISHA) |
| Scaffold_2808 | 2630 | T | C | 75 | 374.77 | CDS | Transition | 0/1 | Nuclear pore complex protein NUP1 (Nuclear pore complex protein NUP136) (Nucleoporin 1) (Nucleoporin 136) |
| Scaffold_2808 | 2665 | T | C | 31 | 187.77 | CDS | Transition | 0/1 | Nuclear pore complex protein NUP1 (Nuclear pore complex protein NUP136) (Nucleoporin 1) (Nucleoporin 136) |