| Variant ID: vg0409086207 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9086207 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 76. )
TCTCCACACCATCAGCCTCATTGTAGAACTCTTTCTCTGATGAATGATTGCAAGGTGAGTATATGACATACTCAGCAAGCCACACAGCAAATATGCAAGT[G/T]
CACAGGATAACAAAGGATGGCATAATAGGGTTGCATTTGCAAAAGCAGCATTTAGCAAACGTTTGAGAATTTGATAAAACAGTTAAGTAATTAAACAATA
TATTGTTTAATTACTTAACTGTTTTATCAAATTCTCAAACGTTTGCTAAATGCTGCTTTTGCAAATGCAACCCTATTATGCCATCCTTTGTTATCCTGTG[C/A]
ACTTGCATATTTGCTGTGTGGCTTGCTGAGTATGTCATATACTCACCTTGCAATCATTCATCAGAGAAAGAGTTCTACAATGAGGCTGATGGTGTGGAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.10% | 0.40% | 1.76% | 76.72% | NA |
| All Indica | 2759 | 1.90% | 0.70% | 1.49% | 95.90% | NA |
| All Japonica | 1512 | 61.00% | 0.00% | 2.25% | 36.77% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.86% | 97.40% | 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 | 1.00% | 1.80% | 1.86% | 95.40% | NA |
| Indica Intermediate | 786 | 2.30% | 0.10% | 1.53% | 96.06% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | 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 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 2.22% | 74.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409086207 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086207 | G -> T | LOC_Os04g16690.1 | downstream_gene_variant ; 4009.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086207 | G -> T | LOC_Os04g16710.1 | downstream_gene_variant ; 2631.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086207 | G -> T | LOC_Os04g16712.1 | downstream_gene_variant ; 4619.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086207 | G -> T | LOC_Os04g16700.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |