| Variant ID: vg0409086204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9086204 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 74. )
AATTCTCCACACCATCAGCCTCATTGTAGAACTCTTTCTCTGATGAATGATTGCAAGGTGAGTATATGACATACTCAGCAAGCCACACAGCAAATATGCA[A/G]
GTGCACAGGATAACAAAGGATGGCATAATAGGGTTGCATTTGCAAAAGCAGCATTTAGCAAACGTTTGAGAATTTGATAAAACAGTTAAGTAATTAAACA
TGTTTAATTACTTAACTGTTTTATCAAATTCTCAAACGTTTGCTAAATGCTGCTTTTGCAAATGCAACCCTATTATGCCATCCTTTGTTATCCTGTGCAC[T/C]
TGCATATTTGCTGTGTGGCTTGCTGAGTATGTCATATACTCACCTTGCAATCATTCATCAGAGAAAGAGTTCTACAATGAGGCTGATGGTGTGGAGAATT
| 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 | 21.10% | 0.40% | 1.84% | 76.64% | NA |
| All Indica | 2759 | 1.80% | 0.70% | 1.49% | 95.94% | NA |
| All Japonica | 1512 | 61.00% | 0.00% | 2.18% | 36.84% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.49% | 97.77% | NA |
| Indica I | 595 | 1.30% | 0.30% | 0.67% | 97.65% | NA |
| Indica II | 465 | 3.70% | 0.20% | 1.72% | 94.41% | NA |
| Indica III | 913 | 0.90% | 1.80% | 1.86% | 95.51% | NA |
| Indica Intermediate | 786 | 2.30% | 0.10% | 1.53% | 96.06% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 4.60% | 0.00% | 5.75% | 89.68% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 1.66% | 30.29% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 8.33% | 90.62% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 1.11% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409086204 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086204 | A -> G | LOC_Os04g16690.1 | downstream_gene_variant ; 4006.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086204 | A -> G | LOC_Os04g16710.1 | downstream_gene_variant ; 2634.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086204 | A -> G | LOC_Os04g16712.1 | downstream_gene_variant ; 4622.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086204 | A -> G | LOC_Os04g16700.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |