| Variant ID: vg0404368261 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4368261 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTGGTTCTTTTGATCCGTGCGGATCTTGTGCTTTTCTCTCTTTGGATTTCTTTTCCCGAACCGATCTAAGCCCTAGGATCGCTCTGATACCAATGTTATA[C/G]
TTTGCACTAGGATCACCTAGGTTAGATCTAGTCGGGTGGTTCTATTTGGGATTGAGGTTTGAACTATAGAGATTGAAAACGGGAGAGGGTTTAGATAGAC
GTCTATCTAAACCCTCTCCCGTTTTCAATCTCTATAGTTCAAACCTCAATCCCAAATAGAACCACCCGACTAGATCTAACCTAGGTGATCCTAGTGCAAA[G/C]
TATAACATTGGTATCAGAGCGATCCTAGGGCTTAGATCGGTTCGGGAAAAGAAATCCAAAGAGAGAAAAGCACAAGATCCGCACGGATCAAAAGAACCAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.50% | 0.10% | 19.28% | 51.12% | NA |
| All Indica | 2759 | 21.60% | 0.00% | 27.47% | 50.96% | NA |
| All Japonica | 1512 | 50.70% | 0.10% | 3.90% | 45.24% | NA |
| Aus | 269 | 2.20% | 1.10% | 21.19% | 75.46% | NA |
| Indica I | 595 | 13.40% | 0.00% | 45.04% | 41.51% | NA |
| Indica II | 465 | 24.30% | 0.00% | 27.96% | 47.74% | NA |
| Indica III | 913 | 23.80% | 0.00% | 17.85% | 58.38% | NA |
| Indica Intermediate | 786 | 23.50% | 0.00% | 25.06% | 51.40% | NA |
| Temperate Japonica | 767 | 87.20% | 0.00% | 0.52% | 12.26% | NA |
| Tropical Japonica | 504 | 7.30% | 0.40% | 8.33% | 83.93% | NA |
| Japonica Intermediate | 241 | 25.30% | 0.00% | 5.39% | 69.29% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 17.71% | 76.04% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 22.22% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404368261 | C -> DEL | N | N | silent_mutation | Average:6.391; most accessible tissue: Callus, score: 9.548 | N | N | N | N |
| vg0404368261 | C -> G | LOC_Os04g08210.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.391; most accessible tissue: Callus, score: 9.548 | N | N | N | N |