| Variant ID: vg0728252659 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 28252659 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 363. )
ATCCAACATGCAAATTTTAACATATTATTCCTCAATTCAATGATCTCATGAGAGAATGATAATACTTGCATGCGCAGCAACACGGCAACTAAATTACTGT[A/C]
CTCGCTTCAGACTACAACAACTATGCAAAGGGTGGACTGTAATTCAAGCAAGGTCGAAGCAAGCAATTACCCACGCGAAGGAATCAGTTAGAGACAACAA
TTGTTGTCTCTAACTGATTCCTTCGCGTGGGTAATTGCTTGCTTCGACCTTGCTTGAATTACAGTCCACCCTTTGCATAGTTGTTGTAGTCTGAAGCGAG[T/G]
ACAGTAATTTAGTTGCCGTGTTGCTGCGCATGCAAGTATTATCATTCTCTCATGAGATCATTGAATTGAGGAATAATATGTTAAAATTTGCATGTTGGAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.50% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.80% | 1.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0728252659 | A -> C | LOC_Os07g47260.1 | downstream_gene_variant ; 2952.0bp to feature; MODIFIER | N | Average:50.903; most accessible tissue: Zhenshan97 root, score: 73.6 | N | N | N | N |
| vg0728252659 | A -> C | LOC_Os07g47270.1 | intron_variant ; MODIFIER | N | Average:50.903; most accessible tissue: Zhenshan97 root, score: 73.6 | N | N | N | N |