| Variant ID: vg0409086123 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9086123 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 63. )
CAATAAAGATCTAAGCAGCGGAAAATAAATAAACGGCGCAGACGGCTCCACTCCACAGGCATCTTGACCAAGGCTACACCTAATTCTCCACACCATCAGC[C/A]
TCATTGTAGAACTCTTTCTCTGATGAATGATTGCAAGGTGAGTATATGACATACTCAGCAAGCCACACAGCAAATATGCAAGTGCACAGGATAACAAAGG
CCTTTGTTATCCTGTGCACTTGCATATTTGCTGTGTGGCTTGCTGAGTATGTCATATACTCACCTTGCAATCATTCATCAGAGAAAGAGTTCTACAATGA[G/T]
GCTGATGGTGTGGAGAATTAGGTGTAGCCTTGGTCAAGATGCCTGTGGAGTGGAGCCGTCTGCGCCGTTTATTTATTTTCCGCTGCTTAGATCTTTATTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.00% | 0.30% | 0.53% | 78.18% | NA |
| All Indica | 2759 | 1.60% | 0.40% | 0.51% | 97.50% | NA |
| All Japonica | 1512 | 61.00% | 0.00% | 0.00% | 38.96% | NA |
| Aus | 269 | 3.00% | 0.00% | 0.00% | 97.03% | NA |
| Indica I | 595 | 1.20% | 0.30% | 0.17% | 98.32% | NA |
| Indica II | 465 | 1.90% | 0.60% | 1.29% | 96.13% | NA |
| Indica III | 913 | 0.80% | 0.70% | 0.44% | 98.14% | NA |
| Indica Intermediate | 786 | 2.50% | 0.10% | 0.38% | 96.95% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.00% | 4.04% | NA |
| Tropical Japonica | 504 | 4.40% | 0.00% | 0.00% | 95.63% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 0.00% | 31.54% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 9.38% | 89.58% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 2.22% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409086123 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086123 | C -> A | LOC_Os04g16690.1 | downstream_gene_variant ; 3925.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086123 | C -> A | LOC_Os04g16710.1 | downstream_gene_variant ; 2715.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086123 | C -> A | LOC_Os04g16712.1 | downstream_gene_variant ; 4703.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086123 | C -> A | LOC_Os04g16700.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |