| Variant ID: vg0135353088 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35353088 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTTGTGCAAATCATAGCGGATTTTGTAAATGGTTAGACATACAACGAAATCGTTGTCTACATTGGGGCAGACAAAATATCTCCTTCGAAATGTTTGTTCA[A/G]
CAAAGGATGTAGCCACCTGCCAGCGATCTCTGCACCCACACTTTGGACGCTTGGACCATTTAGGTAACCCTAATGGATTGTTCCTCCAGTCTAAGCTTGC
GCAAGCTTAGACTGGAGGAACAATCCATTAGGGTTACCTAAATGGTCCAAGCGTCCAAAGTGTGGGTGCAGAGATCGCTGGCAGGTGGCTACATCCTTTG[T/C]
TGAACAAACATTTCGAAGGAGATATTTTGTCTGCCCCAATGTAGACAACGATTTCGTTGTATGTCTAACCATTTACAAAATCCGCTATGATTTGCACAAA
| 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 | 24.70% | 0.10% | 2.41% | 72.79% | NA |
| All Indica | 2759 | 3.00% | 0.00% | 0.33% | 96.67% | NA |
| All Japonica | 1512 | 62.80% | 0.40% | 6.61% | 30.16% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.37% | 98.88% | NA |
| Indica I | 595 | 4.70% | 0.00% | 0.34% | 94.96% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.65% | 98.71% | NA |
| Indica III | 913 | 1.60% | 0.00% | 0.44% | 97.92% | NA |
| Indica Intermediate | 786 | 4.70% | 0.00% | 0.00% | 95.29% | NA |
| Temperate Japonica | 767 | 55.50% | 0.10% | 1.69% | 42.63% | NA |
| Tropical Japonica | 504 | 64.70% | 1.00% | 15.08% | 19.25% | NA |
| Japonica Intermediate | 241 | 82.20% | 0.00% | 4.56% | 13.28% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 4.44% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135353088 | A -> G | LOC_Os01g61080.1 | downstream_gene_variant ; 2443.0bp to feature; MODIFIER | silent_mutation | Average:18.329; most accessible tissue: Zhenshan97 root, score: 41.416 | N | N | N | N |
| vg0135353088 | A -> G | LOC_Os01g61090.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.329; most accessible tissue: Zhenshan97 root, score: 41.416 | N | N | N | N |
| vg0135353088 | A -> DEL | N | N | silent_mutation | Average:18.329; most accessible tissue: Zhenshan97 root, score: 41.416 | N | N | N | N |