| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3962 | 28679 | C | T | 33 | 164.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 29035 | C | T | 11 | 35.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 29239 | T | C | 38 | 716.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 29298 | A | G | 46 | 300.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3969 | 44856 | T | C | 19 | 178.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3969 | 44975 | T | C | 39 | 818.96 | exon | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE1 (Retro element 1) (AtRE1) [Includes: Protease RE1 (EC 3.4.23.-); Reverse transcriptase RE1 (EC 2.7.7.49); Endonuclease RE1] |
| Scaffold_3969 | 45336 | C | T | 12 | 39.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3969 | 46165 | T | C | 21 | 57.77 | CDS | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |
| Scaffold_3971 | 25103 | T | C | 109 | 284.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25104 | T | C | 186 | 781.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25106 | A | G | 250 | 1042.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25117 | T | C | 250 | 59.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25118 | T | C | 250 | 889.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25149 | A | G | 250 | 433.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25194 | A | G | 250 | 681.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25206 | T | C | 249 | 1039.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25208 | T | C | 250 | 2032.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25254 | A | G | 250 | 320.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3971 | 25549 | G | A | 184 | 6359.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3975 | 35860 | T | C | 98 | 74.77 | exon | Transition | 0/1 | Phosphate transporter PHO1 homolog 3 (Protein PHO1 homolog 3) (AtPHO1;H3) |