| Variant ID: vg0409086131 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9086131 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.02, others allele: 0.00, population size: 63. )
ATCTAAGCAGCGGAAAATAAATAAACGGCGCAGACGGCTCCACTCCACAGGCATCTTGACCAAGGCTACACCTAATTCTCCACACCATCAGCCTCATTGT[A/T]
GAACTCTTTCTCTGATGAATGATTGCAAGGTGAGTATATGACATACTCAGCAAGCCACACAGCAAATATGCAAGTGCACAGGATAACAAAGGATGGCATA
TATGCCATCCTTTGTTATCCTGTGCACTTGCATATTTGCTGTGTGGCTTGCTGAGTATGTCATATACTCACCTTGCAATCATTCATCAGAGAAAGAGTTC[T/A]
ACAATGAGGCTGATGGTGTGGAGAATTAGGTGTAGCCTTGGTCAAGATGCCTGTGGAGTGGAGCCGTCTGCGCCGTTTATTTATTTTCCGCTGCTTAGAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.00% | 0.60% | 1.84% | 76.51% | NA |
| All Indica | 2759 | 1.60% | 1.10% | 1.63% | 95.72% | NA |
| All Japonica | 1512 | 60.90% | 0.00% | 1.92% | 37.17% | NA |
| Aus | 269 | 3.00% | 0.00% | 0.74% | 96.28% | NA |
| Indica I | 595 | 0.80% | 0.70% | 1.01% | 97.48% | NA |
| Indica II | 465 | 1.90% | 0.90% | 2.58% | 94.62% | NA |
| Indica III | 913 | 0.90% | 2.20% | 1.53% | 95.40% | NA |
| Indica Intermediate | 786 | 2.80% | 0.10% | 1.65% | 95.42% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 4.40% | 0.00% | 5.16% | 90.48% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 1.24% | 30.71% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 8.33% | 89.58% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 3.33% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409086131 | A -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086131 | A -> T | LOC_Os04g16690.1 | downstream_gene_variant ; 3933.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086131 | A -> T | LOC_Os04g16710.1 | downstream_gene_variant ; 2707.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086131 | A -> T | LOC_Os04g16712.1 | downstream_gene_variant ; 4695.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409086131 | A -> T | LOC_Os04g16700.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |