| Variant ID: vg0404368259 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4368259 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, T: 0.27, others allele: 0.00, population size: 45. )
TTTTGGTTCTTTTGATCCGTGCGGATCTTGTGCTTTTCTCTCTTTGGATTTCTTTTCCCGAACCGATCTAAGCCCTAGGATCGCTCTGATACCAATGTTA[T/G]
ACTTTGCACTAGGATCACCTAGGTTAGATCTAGTCGGGTGGTTCTATTTGGGATTGAGGTTTGAACTATAGAGATTGAAAACGGGAGAGGGTTTAGATAG
CTATCTAAACCCTCTCCCGTTTTCAATCTCTATAGTTCAAACCTCAATCCCAAATAGAACCACCCGACTAGATCTAACCTAGGTGATCCTAGTGCAAAGT[A/C]
TAACATTGGTATCAGAGCGATCCTAGGGCTTAGATCGGTTCGGGAAAAGAAATCCAAAGAGAGAAAAGCACAAGATCCGCACGGATCAAAAGAACCAAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.00% | 2.00% | 8.06% | 71.88% | NA |
| All Indica | 2759 | 2.90% | 3.00% | 12.18% | 81.88% | NA |
| All Japonica | 1512 | 49.90% | 0.30% | 0.99% | 48.81% | NA |
| Aus | 269 | 0.40% | 1.10% | 7.43% | 91.08% | NA |
| Indica I | 595 | 1.70% | 1.70% | 13.45% | 83.19% | NA |
| Indica II | 465 | 4.90% | 1.90% | 13.33% | 79.78% | NA |
| Indica III | 913 | 1.50% | 5.00% | 8.54% | 84.88% | NA |
| Indica Intermediate | 786 | 4.20% | 2.40% | 14.76% | 78.63% | NA |
| Temperate Japonica | 767 | 87.10% | 0.00% | 0.00% | 12.91% | NA |
| Tropical Japonica | 504 | 5.60% | 0.80% | 2.18% | 91.47% | NA |
| Japonica Intermediate | 241 | 24.50% | 0.00% | 1.66% | 73.86% | NA |
| VI/Aromatic | 96 | 1.00% | 2.10% | 3.12% | 93.75% | NA |
| Intermediate | 90 | 16.70% | 3.30% | 7.78% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404368259 | T -> DEL | N | N | silent_mutation | Average:6.391; most accessible tissue: Callus, score: 9.548 | N | N | N | N |
| vg0404368259 | T -> G | LOC_Os04g08210.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.391; most accessible tissue: Callus, score: 9.548 | N | N | N | N |