| Variant ID: vg0522745487 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22745487 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 277. )
TCCTCCTCTTCCTCCCCTTCCTCTTCTTCGTTGTCGTTGTCGTCGTCGTCGTCGTCCGAGGAAGACGACGACGAGCTATCAGAGTGATCTGATTTTGGTG[C/T]
AGGGGAGGCAGATGGAGCTGGGGCTGGGACGCTGGCAGCTGGTGGATCCGGTGGCAGTGAGGTCAGGAAGCCCAGCGTCATGACAACGTCGGCCATCAAC
GTTGATGGCCGACGTTGTCATGACGCTGGGCTTCCTGACCTCACTGCCACCGGATCCACCAGCTGCCAGCGTCCCAGCCCCAGCTCCATCTGCCTCCCCT[G/A]
CACCAAAATCAGATCACTCTGATAGCTCGTCGTCGTCTTCCTCGGACGACGACGACGACGACAACGACAACGAAGAAGAGGAAGGGGAGGAAGAGGAGGA
| 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 | 99.40% | 0.50% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.00% | 0.80% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 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 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.00% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0522745487 | C -> T | LOC_Os05g38770.1 | missense_variant ; p.Ala378Thr; MODERATE | N | Average:49.232; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg0522745487 | C -> T | LOC_Os05g38760.1 | upstream_gene_variant ; 1035.0bp to feature; MODIFIER | N | Average:49.232; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |