| Variant ID: vg0409081698 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9081698 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 309. )
TATTTCTTATGGATGGTTCTTATGCATAAGGATAACTCATCCTAAGAACATCTATTAGGACTACTCCCATAGTATATAATGCCCACTTTAGAGGTCTAAG[A/G]
TCCTCCCCTGCGACTACATTAATTGTAGGTGCCCTAAGATTCACATACCAGAGGGGCTTCCCATACTTTTTTTAAGGTAAAACAAAGGCCAGTGTATTGA
TCAATACACTGGCCTTTGTTTTACCTTAAAAAAAGTATGGGAAGCCCCTCTGGTATGTGAATCTTAGGGCACCTACAATTAATGTAGTCGCAGGGGAGGA[T/C]
CTTAGACCTCTAAAGTGGGCATTATATACTATGGGAGTAGTCCTAATAGATGTTCTTAGGATGAGTTATCCTTATGCATAAGAACCATCCATAAGAAATA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.60% | 0.07% | 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 | 98.70% | 1.20% | 0.13% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081698 | A -> G | LOC_Os04g16680.1 | upstream_gene_variant ; 3810.0bp to feature; MODIFIER | N | Average:60.04; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| vg0409081698 | A -> G | LOC_Os04g16700.1 | downstream_gene_variant ; 3366.0bp to feature; MODIFIER | N | Average:60.04; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |
| vg0409081698 | A -> G | LOC_Os04g16690.1 | intron_variant ; MODIFIER | N | Average:60.04; most accessible tissue: Minghui63 flag leaf, score: 80.786 | N | N | N | N |