| Variant ID: vg0415572547 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15572547 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 345. )
TTTATACCACTCAAACATGTTAGCAAATCAATCTTCTCTTCTTTCGAGAGAGTGTAGCAGGCTGGAGGAAGGTAAACCCTGCCAGATTCCGTGGTTATGG[G/A]
ATGTAGCTCCGACCGAACACCCATATCTTCCAGATCTCGTCGGGCGTTGAGACCATCCTTTGTAGTACCTGGGTTAAGCAGTAATCCCATTAAACTCTCG
CGAGAGTTTAATGGGATTACTGCTTAACCCAGGTACTACAAAGGATGGTCTCAACGCCCGACGAGATCTGGAAGATATGGGTGTTCGGTCGGAGCTACAT[C/T]
CCATAACCACGGAATCTGGCAGGGTTTACCTTCCTCCAGCCTGCTACACTCTCTCGAAAGAAGAGAAGATTGATTTGCTAACATGTTTGAGTGGTATAAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.50% | 0.00% | 6.86% | 21.67% | NA |
| All Indica | 2759 | 73.30% | 0.00% | 11.02% | 15.69% | NA |
| All Japonica | 1512 | 78.40% | 0.00% | 0.46% | 21.10% | NA |
| Aus | 269 | 3.70% | 0.00% | 2.97% | 93.31% | NA |
| Indica I | 595 | 90.80% | 0.00% | 0.00% | 9.24% | NA |
| Indica II | 465 | 67.50% | 0.00% | 4.52% | 27.96% | NA |
| Indica III | 913 | 61.30% | 0.00% | 25.30% | 13.36% | NA |
| Indica Intermediate | 786 | 77.40% | 0.00% | 6.62% | 16.03% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.78% | 39.50% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.41% | 4.15% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 5.56% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415572547 | G -> A | LOC_Os04g26690.1 | missense_variant ; p.Pro512Ser; MODERATE | N | Average:4.422; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0415572547 | G -> A | LOC_Os04g26670.1 | downstream_gene_variant ; 4522.0bp to feature; MODIFIER | N | Average:4.422; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0415572547 | G -> A | LOC_Os04g26680.1 | downstream_gene_variant ; 2221.0bp to feature; MODIFIER | N | Average:4.422; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |