| Variant ID: vg0522745226 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 22745226 |
| Reference Allele: C | Alternative Allele: CA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )
TTTAAACCATTTAGCATGTTCGTTATTATCACAACAAAAAACATTTACTTGTTGAAGCCCCACCCCCCAATTTACATTGTCCACGGCCTCTGAGAAACGT[C/CA]
AAAAAAAATAACTCAGGTATACAACTCCTTCCACATCAAACCATCTCTGGTTTAATCACCTGATCCTTCAAATTAAGCGTTTAACATTTGATCTTCTTCT
AGAAGAAGATCAAATGTTAAACGCTTAATTTGAAGGATCAGGTGATTAAACCAGAGATGGTTTGATGTGGAAGGAGTTGTATACCTGAGTTATTTTTTTT[G/TG]
ACGTTTCTCAGAGGCCGTGGACAATGTAAATTGGGGGGTGGGGCTTCAACAAGTAAATGTTTTTTGTTGTGATAATAACGAACATGCTAAATGGTTTAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 90.90% | 9.10% | 0.00% | 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 | 67.70% | 32.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.70% | 5.30% | 0.00% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0522745226 | C -> CA | LOC_Os05g38770.1 | 3_prime_UTR_variant ; 138.0bp to feature; MODIFIER | silent_mutation | Average:37.024; most accessible tissue: Zhenshan97 young leaf, score: 66.32 | N | N | N | N |
| vg0522745226 | C -> CA | LOC_Os05g38760.1 | upstream_gene_variant ; 775.0bp to feature; MODIFIER | silent_mutation | Average:37.024; most accessible tissue: Zhenshan97 young leaf, score: 66.32 | N | N | N | N |