| Variant ID: vg0420973001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20973001 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 350. )
ACAAATTCAGTGCCGTGATTCTTTGCTATTTCGGGTGCGAGAGGTGGCTGAATGCCTGAGTTCATAGTTGCAGGCATAGCTACATCTTATGTTTTAAGTT[A/G]
TGTATGTATACAAAGCCCCTTGCACCAAAAGAGCTGAAAACTGCTCAACTGGCTTTAATTTGTCTGCGGCTATAATTTTGCACGGCAGTTGTGCATATTG
CAATATGCACAACTGCCGTGCAAAATTATAGCCGCAGACAAATTAAAGCCAGTTGAGCAGTTTTCAGCTCTTTTGGTGCAAGGGGCTTTGTATACATACA[T/C]
AACTTAAAACATAAGATGTAGCTATGCCTGCAACTATGAACTCAGGCATTCAGCCACCTCTCGCACCCGAAATAGCAAAGAATCACGGCACTGAATTTGT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.60% | 8.80% | 1.74% | 40.92% | NA |
| All Indica | 2759 | 40.10% | 0.80% | 1.49% | 57.63% | NA |
| All Japonica | 1512 | 70.40% | 21.20% | 1.39% | 7.01% | NA |
| Aus | 269 | 4.50% | 20.40% | 1.86% | 73.23% | NA |
| Indica I | 595 | 77.50% | 0.00% | 1.18% | 21.34% | NA |
| Indica II | 465 | 15.50% | 2.20% | 1.51% | 80.86% | NA |
| Indica III | 913 | 35.80% | 0.40% | 1.20% | 62.54% | NA |
| Indica Intermediate | 786 | 31.20% | 1.10% | 2.04% | 65.65% | NA |
| Temperate Japonica | 767 | 97.70% | 2.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 23.40% | 55.60% | 3.57% | 17.46% | NA |
| Japonica Intermediate | 241 | 81.70% | 10.00% | 1.24% | 7.05% | NA |
| VI/Aromatic | 96 | 65.60% | 0.00% | 13.54% | 20.83% | NA |
| Intermediate | 90 | 56.70% | 17.80% | 2.22% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420973001 | A -> DEL | N | N | silent_mutation | Average:47.91; most accessible tissue: Zhenshan97 flower, score: 74.953 | N | N | N | N |
| vg0420973001 | A -> G | LOC_Os04g34670.1 | 3_prime_UTR_variant ; 206.0bp to feature; MODIFIER | silent_mutation | Average:47.91; most accessible tissue: Zhenshan97 flower, score: 74.953 | N | N | N | N |
| vg0420973001 | A -> G | LOC_Os04g34680.1 | downstream_gene_variant ; 3362.0bp to feature; MODIFIER | silent_mutation | Average:47.91; most accessible tissue: Zhenshan97 flower, score: 74.953 | N | N | N | N |