| Variant ID: vg0804463836 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463836 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 122. )
GTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCAGTTTTTTTGAAAATTTATATCCCAATAGGT[T/C]
CTATGAATATCATACTATTTATAAGATTTTATTTGATTTTTTCCTTTTTTATCAATTTAAATTTGAATTTGGATGAAACTCATCGAAATCTCAGACGGCT
AGCCGTCTGAGATTTCGATGAGTTTCATCCAAATTCAAATTTAAATTGATAAAAAAGGAAAAAATCAAATAAAATCTTATAAATAGTATGATATTCATAG[A/G]
ACCTATTGGGATATAAATTTTCAAAAAAACTGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.60% | 0.60% | 0.36% | 63.44% | NA |
| All Indica | 2759 | 6.00% | 1.00% | 0.33% | 92.71% | NA |
| All Japonica | 1512 | 95.00% | 0.00% | 0.20% | 4.83% | NA |
| Aus | 269 | 10.00% | 0.00% | 0.74% | 89.22% | NA |
| Indica I | 595 | 9.40% | 1.30% | 0.34% | 88.91% | NA |
| Indica II | 465 | 6.20% | 1.70% | 0.43% | 91.61% | NA |
| Indica III | 913 | 2.70% | 0.50% | 0.00% | 96.71% | NA |
| Indica Intermediate | 786 | 7.00% | 0.80% | 0.64% | 91.60% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.26% | 1.56% | NA |
| Tropical Japonica | 504 | 88.70% | 0.00% | 0.20% | 11.11% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 1.04% | 80.21% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 2.22% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463836 | T -> C | LOC_Os08g07900.1 | upstream_gene_variant ; 3613.0bp to feature; MODIFIER | silent_mutation | Average:13.931; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0804463836 | T -> C | LOC_Os08g07910.1 | upstream_gene_variant ; 2715.0bp to feature; MODIFIER | silent_mutation | Average:13.931; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0804463836 | T -> C | LOC_Os08g07930.1 | upstream_gene_variant ; 2193.0bp to feature; MODIFIER | silent_mutation | Average:13.931; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0804463836 | T -> C | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.931; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0804463836 | T -> DEL | N | N | silent_mutation | Average:13.931; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |