| Variant ID: vg0825015887 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 25015887 |
| Reference Allele: C | Alternative Allele: CA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )
ATGAAACCACAACCTCTCATACAAGATCTTTAGCATTTCTTATGCTTTTGTCACTTGTACAATACAAACTTTAAAGTAGAACTATCAAGTAAATCACTAG[C/CA]
AAAAAAGGTTAAAAGTATAAAGAAGAGAAAGGCAGGAAAGAGAAAACATTCTTCTTTTCCTTAACCACTTCCTCTTTCTCTCACACACACACACACTAGG
CCTAGTGTGTGTGTGTGTGAGAGAAAGAGGAAGTGGTTAAGGAAAAGAAGAATGTTTTCTCTTTCCTGCCTTTCTCTTCTTTATACTTTTAACCTTTTTT[G/TG]
CTAGTGATTTACTTGATAGTTCTACTTTAAAGTTTGTATTGTACAAGTGACAAAAGCATAAGAAATGCTAAAGATCTTGTATGAGAGGTTGTGGTTTCAT
| 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 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0825015887 | C -> CA | LOC_Os08g39550.1 | 3_prime_UTR_variant ; 288.0bp to feature; MODIFIER | silent_mutation | Average:68.689; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |
| vg0825015887 | C -> CA | LOC_Os08g39540.1 | downstream_gene_variant ; 2456.0bp to feature; MODIFIER | silent_mutation | Average:68.689; most accessible tissue: Zhenshan97 panicle, score: 83.904 | N | N | N | N |