| Variant ID: vg1201984307 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1984307 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 340. )
TGGTGAATTAGAGGAAGCGTTCAGTGTATTCTATTTTGACGGTGATGGGTTCATATGTTCCTTAGAGTTGCAAAATGTGATGATAAGGATGCTAGGTATG[A/G]
GGACTGTGAAAAGATGATTCATGTTTTTGACAAAGATGGTGATGGCAGGATTAGATTGGATGAGTTCAGAGCTGTGTGACTAAAACCTCTTTCTTGTTAA
TTAACAAGAAAGAGGTTTTAGTCACACAGCTCTGAACTCATCCAATCTAATCCTGCCATCACCATCTTTGTCAAAAACATGAATCATCTTTTCACAGTCC[T/C]
CATACCTAGCATCCTTATCATCACATTTTGCAACTCTAAGGAACATATGAACCCATCACCGTCAAAATAGAATACACTGAACGCTTCCTCTAATTCACCA
| 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 | 99.70% | 0.10% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.60% | 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 | 99.20% | 0.00% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.00% | 0.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1201984307 | A -> G | LOC_Os12g04680.1 | missense_variant ; p.Glu55Gly; MODERATE | N | Average:62.863; most accessible tissue: Zhenshan97 root, score: 76.397 | N | N | N | N |
| vg1201984307 | A -> G | LOC_Os12g04670.1 | upstream_gene_variant ; 1234.0bp to feature; MODIFIER | N | Average:62.863; most accessible tissue: Zhenshan97 root, score: 76.397 | N | N | N | N |
| vg1201984307 | A -> G | LOC_Os12g04690.1 | upstream_gene_variant ; 1944.0bp to feature; MODIFIER | N | Average:62.863; most accessible tissue: Zhenshan97 root, score: 76.397 | N | N | N | N |