| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2646 | 55773 | C | T | 21 | 43.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2646 | 80059 | C | T | 21 | 46.77 | exon | Transition | 0/1 | BTB/POZ domain-containing protein At3g09030 |
| Scaffold_2651 | 30105 | T | C | 17 | 34.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2654 | 34349 | T | C | 13 | 126.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2659 | 713 | A | G | 11 | 30.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2660 | 29172 | G | A | 106 | 38.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2660 | 78880 | T | C | 20 | 45.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2667 | 59392 | T | C | 18 | 123.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2677 | 5044 | A | G | 15 | 46.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2677 | 111488 | G | A | 25 | 31.77 | CDS | Transition | 0/1 | PAP-specific phosphatase HAL2-like (3'(2'),5'-bisphosphate nucleotidase) (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrolase) (DPNPase) (Halotolerance protein) |
| Scaffold_2677 | 138623 | A | G | 16 | 43.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2679 | 15835 | A | G | 24 | 52.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2679 | 43559 | G | A | 10 | 32.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2679 | 50684 | G | A | 13 | 49.77 | CDS | Transition | 0/1 | Probable protein S-acyltransferase 14 (EC 2.3.1.225) (Probable palmitoyltransferase At3g60800) (Zinc finger DHHC domain-containing protein At3g60800) |
| Scaffold_2681 | 54019 | A | G | 13 | 43.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2681 | 152818 | T | C | 26 | 589.77 | CDS | Transition | 0/1 | Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (26S proteasome regulatory subunit RPN3) (Nuclear antigen 21D7) |
| Scaffold_2683 | 65760 | G | A | 11 | 274.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2683 | 80938 | T | C | 13 | 51.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2683 | 100582 | A | G | 32 | 93.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2683 | 101352 | A | G | 16 | 77.77 | CDS | Transition | 0/1 | Unannotated |