| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_53 | 1502358 | T | G | 15 | 33.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_53 | 1770683 | T | A | 14 | 107.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_53 | 1810621 | T | G | 20 | 278.78 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 550686 | T | A | 250 | 5457.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 552825 | A | C | 10 | 174.79 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 952756 | A | C | 18 | 40.77 | CDS | Transversion | 0/1 | Trafficking protein particle complex II-specific subunit 130 homolog (AtTRS130) (TRAPP II-specific subunit 130 homolog) |
| Scaffold_54 | 1018319 | T | A | 18 | 368.22 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 1165546 | C | G | 10 | 61.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 1166695 | G | T | 12 | 324.03 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 1166697 | A | C | 11 | 277.9 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_54 | 1298595 | G | T | 13 | 61.77 | CDS | Transversion | 0/1 | tRNAse Z TRZ4, mitochondrial (EC 3.1.26.11) (Long tRNase Z 2) (tRNase ZL2) (AthTRZL2) |
| Scaffold_54 | 1298596 | G | C | 13 | 58.77 | CDS | Transversion | 0/1 | tRNAse Z TRZ4, mitochondrial (EC 3.1.26.11) (Long tRNase Z 2) (tRNase ZL2) (AthTRZL2) |
| Scaffold_54 | 1298695 | T | A | 21 | 34.77 | CDS | Transversion | 0/1 | tRNAse Z TRZ4, mitochondrial (EC 3.1.26.11) (Long tRNase Z 2) (tRNase ZL2) (AthTRZL2) |
| Scaffold_54 | 1538351 | C | A | 23 | 31.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_55 | 217945 | G | C | 32 | 225.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_55 | 273374 | G | C | 24 | 42.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_55 | 333127 | C | A | 14 | 61.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_55 | 448276 | G | T | 13 | 70.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_55 | 936391 | C | G | 12 | 39.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_55 | 1001444 | G | C | 24 | 74.77 | CDS | Transversion | 0/1 | Unannotated |