| Variant ID: vg0125055886 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25055886 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTTTTGCTATATTTTTAAAGTGTCGATTCAATCAAACCAAATATTTGACAATACCTTTTCTTTACAAACTAAATGGAGAATTAATTTATTGATATGGCT[A/T]
AATTATTTTTTGGTGGCATGGTTGATTGGTATAAACCAAACATGCCATTTTTTTTAAAAAAAAAGCCTACAATGCATGATATGAACATCACAAGATCGAC
GTCGATCTTGTGATGTTCATATCATGCATTGTAGGCTTTTTTTTTAAAAAAAATGGCATGTTTGGTTTATACCAATCAACCATGCCACCAAAAAATAATT[T/A]
AGCCATATCAATAAATTAATTCTCCATTTAGTTTGTAAAGAAAAGGTATTGTCAAATATTTGGTTTGATTGAATCGACACTTTAAAAATATAGCAAAACG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.60% | 3.20% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 90.30% | 9.10% | 0.60% | 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 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 97.30% | 1.70% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 76.60% | 23.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.70% | 2.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 11.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125055886 | A -> T | LOC_Os01g43720.1 | 3_prime_UTR_variant ; 662.0bp to feature; MODIFIER | silent_mutation | Average:69.264; most accessible tissue: Zhenshan97 root, score: 88.474 | N | N | N | N |
| vg0125055886 | A -> T | LOC_Os01g43740.1 | upstream_gene_variant ; 4878.0bp to feature; MODIFIER | silent_mutation | Average:69.264; most accessible tissue: Zhenshan97 root, score: 88.474 | N | N | N | N |