| Variant ID: vg0125055855 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25055855 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAGTACAATTTTGATGAAGTTGCAAAATATTCGTTTTGCTATATTTTTAAAGTGTCGATTCAATCAAACCAAATATTTGACAATACCTTTTCTTTACAAA[C/T]
TAAATGGAGAATTAATTTATTGATATGGCTAAATTATTTTTTGGTGGCATGGTTGATTGGTATAAACCAAACATGCCATTTTTTTTAAAAAAAAAGCCTA
TAGGCTTTTTTTTTAAAAAAAATGGCATGTTTGGTTTATACCAATCAACCATGCCACCAAAAAATAATTTAGCCATATCAATAAATTAATTCTCCATTTA[G/A]
TTTGTAAAGAAAAGGTATTGTCAAATATTTGGTTTGATTGAATCGACACTTTAAAAATATAGCAAAACGAATATTTTGCAACTTCATCAAAATTGTACTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.90% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 96.80% | 2.70% | 0.46% | 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 | 94.50% | 4.60% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125055855 | C -> T | LOC_Os01g43720.1 | 3_prime_UTR_variant ; 693.0bp to feature; MODIFIER | silent_mutation | Average:64.799; most accessible tissue: Zhenshan97 root, score: 88.238 | N | N | N | N |
| vg0125055855 | C -> T | LOC_Os01g43740.1 | upstream_gene_variant ; 4909.0bp to feature; MODIFIER | silent_mutation | Average:64.799; most accessible tissue: Zhenshan97 root, score: 88.238 | N | N | N | N |