| Variant ID: vg0826584209 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584209 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 128. )
ATGAGAAATTTGACAAAACATTGACATCTGCAGGCTTTGCAGTCAATGAGGCAGATAAATGTGTGTACTATCGCCATGGTGGGGGTGAGGGAGTTATTTT[G/A]
TGCTTGTATGTTGATGACATACTGATATTTGGGACAAACCTTGAGGTGATAAATGAGGTTAAATCATTCTTGTCTCAAAATTTTGATATGAAAGATTTGG
CCAAATCTTTCATATCAAAATTTTGAGACAAGAATGATTTAACCTCATTTATCACCTCAAGGTTTGTCCCAAATATCAGTATGTCATCAACATACAAGCA[C/T]
AAAATAACTCCCTCACCCCCACCATGGCGATAGTACACACATTTATCTGCCTCATTGACTGCAAAGCCTGCAGATGTCAATGTTTTGTCAAATTTCTCAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.80% | 0.80% | 19.97% | 77.49% | NA |
| All Indica | 2759 | 0.20% | 1.20% | 13.05% | 85.54% | NA |
| All Japonica | 1512 | 4.80% | 0.00% | 30.89% | 64.29% | NA |
| Aus | 269 | 0.00% | 0.70% | 7.81% | 91.45% | NA |
| Indica I | 595 | 0.20% | 0.70% | 8.24% | 90.92% | NA |
| Indica II | 465 | 0.00% | 0.90% | 5.81% | 93.33% | NA |
| Indica III | 913 | 0.30% | 2.10% | 21.03% | 76.56% | NA |
| Indica Intermediate | 786 | 0.30% | 0.80% | 11.70% | 87.28% | NA |
| Temperate Japonica | 767 | 5.50% | 0.00% | 23.99% | 70.53% | NA |
| Tropical Japonica | 504 | 5.00% | 0.00% | 42.06% | 52.98% | NA |
| Japonica Intermediate | 241 | 2.50% | 0.00% | 29.46% | 68.05% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 70.83% | 23.96% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 31.11% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584209 | G -> A | LOC_Os08g42090.1 | synonymous_variant ; p.Leu984Leu; LOW | synonymous_codon | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0826584209 | G -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |