| Variant ID: vg0409586432 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586432 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: Unkown |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 300. )
TAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTT[T/C]
AATCTAACAAAACCCGAGAAACCCTGAAGGGGTAACTAGCTATATATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCAGCTTGGG
CCCAAGCTGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATATATAGCTAGTTACCCCTTCAGGGTTTCTCGGGTTTTGTTAGATT[A/G]
AAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.60% | 0.00% | 11.28% | 46.09% | NA |
| All Indica | 2759 | 9.40% | 0.00% | 18.56% | 72.06% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Aus | 269 | 32.30% | 0.00% | 4.83% | 62.83% | NA |
| Indica I | 595 | 8.90% | 0.00% | 14.79% | 76.30% | NA |
| Indica II | 465 | 10.50% | 0.00% | 11.40% | 78.06% | NA |
| Indica III | 913 | 6.70% | 0.00% | 19.82% | 73.49% | NA |
| Indica Intermediate | 786 | 12.20% | 0.00% | 24.17% | 63.61% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 4.17% | 3.12% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 4.44% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586432 | T -> C | LOC_Os04g17510.1 | upstream_gene_variant ; 1741.0bp to feature; MODIFIER | N | Average:6.646; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |
| vg0409586432 | T -> C | LOC_Os04g17530.1 | downstream_gene_variant ; 1806.0bp to feature; MODIFIER | N | Average:6.646; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |
| vg0409586432 | T -> C | LOC_Os04g17540.1 | downstream_gene_variant ; 4265.0bp to feature; MODIFIER | N | Average:6.646; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |
| vg0409586432 | T -> C | LOC_Os04g17520.1 | intron_variant ; MODIFIER | N | Average:6.646; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |