| Variant ID: vg0409854438 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9854438 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )
ATGGGCTTGTAACCTCATTTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAAGCTGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCC[T/A]
CCCACCCCTATATATAGCTAGTTACCCCTTCAGGGTTTCTGGGGTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTA
TAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAACCCCAGAAACCCTGAAGGGGTAACTAGCTATATATAGGGGTGGG[A/T]
GGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCAGCTTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAAATGAGGTTACAAGCCCAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.10% | 0.40% | 8.57% | 64.01% | NA |
| All Indica | 2759 | 11.10% | 0.40% | 12.50% | 75.97% | NA |
| All Japonica | 1512 | 61.50% | 0.00% | 0.86% | 37.63% | NA |
| Aus | 269 | 4.80% | 1.50% | 14.50% | 79.18% | NA |
| Indica I | 595 | 13.60% | 0.20% | 7.23% | 78.99% | NA |
| Indica II | 465 | 12.00% | 0.20% | 6.67% | 81.08% | NA |
| Indica III | 913 | 8.10% | 0.50% | 19.61% | 71.74% | NA |
| Indica Intermediate | 786 | 12.10% | 0.60% | 11.70% | 75.57% | NA |
| Temperate Japonica | 767 | 96.30% | 0.00% | 0.00% | 3.65% | NA |
| Tropical Japonica | 504 | 4.80% | 0.00% | 1.19% | 94.05% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.00% | 2.90% | 27.80% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 4.44% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409854438 | T -> DEL | N | N | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854438 | T -> A | LOC_Os04g17910.1 | upstream_gene_variant ; 3743.0bp to feature; MODIFIER | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854438 | T -> A | LOC_Os04g17930.1 | downstream_gene_variant ; 1699.0bp to feature; MODIFIER | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |
| vg0409854438 | T -> A | LOC_Os04g17920.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.228; most accessible tissue: Zhenshan97 flag leaf, score: 10.769 | N | N | N | N |