| Variant ID: vg0426638634 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 26638634 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 322. )
CCTGTGTCCTGCTTCAAAACCCCCCTGTTTGCTTGTTGCTGCTCTCGTTTTTTTCTTTTTTTTTTCAAATGCACCTTGATTTAAGGGAAGGGGAGAAGGG[A/AT]
TTTTTTTTGTTTCCTACTATTTGCAAAGTGTTGTTCAGCTTCAGGACGATAGATGAAGCCTGTTTGAGCTTTTGTGTTTTTTCGTCAAATGTACCTTGTC
GACAAGGTACATTTGACGAAAAAACACAAAAGCTCAAACAGGCTTCATCTATCGTCCTGAAGCTGAACAACACTTTGCAAATAGTAGGAAACAAAAAAAA[T/AT]
CCCTTCTCCCCTTCCCTTAAATCAAGGTGCATTTGAAAAAAAAAAGAAAAAAACGAGAGCAGCAACAAGCAAACAGGGGGGTTTTGAAGCAGGACACAGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 54.30% | 45.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426638634 | A -> AT | LOC_Os04g45030.1 | downstream_gene_variant ; 3536.0bp to feature; MODIFIER | silent_mutation | Average:59.867; most accessible tissue: Zhenshan97 flower, score: 80.006 | N | N | N | N |
| vg0426638634 | A -> AT | LOC_Os04g45020.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.867; most accessible tissue: Zhenshan97 flower, score: 80.006 | N | N | N | N |