| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3942 | 33804 | C | T | 42 | 683.77 | CDS | 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 | 44975 | T | C | 102 | 2829.77 | exon | Transition | 1/1 | 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_12 | 1687011 | T | C | 10 | 69.77 | 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_2921 | 42850 | G | A | 16 | 179.77 | 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_2921 | 42872 | T | C | 21 | 131.77 | 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_3185 | 520 | T | C | 19 | 57.77 | exon | 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_3185 | 542 | A | G | 16 | 118.77 | exon | 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_3185 | 748 | G | A | 12 | 229.84 | exon | Transition | 1/1 | 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_3185 | 756 | G | A | 12 | 228.84 | exon | Transition | 1/1 | 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_3894 | 39930 | C | T | 17 | 83.77 | noncoding | 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_3969 | 46165 | T | C | 83 | 30.77 | 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_3969 | 46190 | A | G | 64 | 1659.84 | CDS | Transition | 1/1 | 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_3969 | 46279 | T | C | 35 | 837.77 | 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_3969 | 46345 | T | C | 35 | 692.78 | 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_3969 | 46381 | C | T | 19 | 36.77 | 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_143 | 495746 | T | C | 16 | 363.77 | exon | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_143 | 495752 | C | T | 16 | 293.77 | exon | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_143 | 495875 | G | A | 11 | 192.88 | exon | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_164 | 297497 | C | T | 11 | 235.84 | CDS | Transition | 1/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_356 | 73395 | T | C | 17 | 477.77 | noncoding | Transition | 1/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |