| Variant ID: vg0815410076 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15410076 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 122. )
ACTCCACATTTGCTGGATCCACAGCTACTCCTTGAGCATTCACGATGTGACCAAGAAACTGAACTTCCTTAAGCCAGAAGTCGCACTTGCTGAACTTGGC[A/G]
TATAGCTGGTGCTCTTTTAACTTTTCAAGTACCAGCCGAAGATGCTGCTCATGTTCTTCCTCGGACTTGGAGTAGATAAGTATGTCATCGATGAAAACCA
TGGTTTTCATCGATGACATACTTATCTACTCCAAGTCCGAGGAAGAACATGAGCAGCATCTTCGGCTGGTACTTGAAAAGTTAAAAGAGCACCAGCTATA[T/C]
GCCAAGTTCAGCAAGTGCGACTTCTGGCTTAAGGAAGTTCAGTTTCTTGGTCACATCGTGAATGCTCAAGGAGTAGCTGTGGATCCAGCAAATGTGGAGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.50% | 0.10% | 10.98% | 68.37% | NA |
| All Indica | 2759 | 0.90% | 0.00% | 11.78% | 87.28% | NA |
| All Japonica | 1512 | 60.40% | 0.50% | 5.95% | 33.13% | NA |
| Aus | 269 | 1.50% | 0.00% | 34.57% | 63.94% | NA |
| Indica I | 595 | 0.30% | 0.00% | 0.50% | 99.16% | NA |
| Indica II | 465 | 1.50% | 0.00% | 8.17% | 90.32% | NA |
| Indica III | 913 | 0.30% | 0.00% | 20.26% | 79.41% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 12.60% | 85.62% | NA |
| Temperate Japonica | 767 | 84.50% | 0.00% | 2.35% | 13.17% | NA |
| Tropical Japonica | 504 | 27.40% | 1.40% | 8.73% | 62.50% | NA |
| Japonica Intermediate | 241 | 53.10% | 0.00% | 11.62% | 35.27% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 3.12% | 94.79% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 8.89% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815410076 | A -> G | LOC_Os08g25330.1 | synonymous_variant ; p.Tyr770Tyr; LOW | synonymous_codon | Average:4.467; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0815410076 | A -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:4.467; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |