| Variant ID: vg0802222500 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2222500 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.85, G: 0.15, others allele: 0.00, population size: 82. )
CTGAGTTGGTGTTGGTAGGATTCTGAGGACACTGTCTGGCATAGTGACCCATCTGGTTGCACCGGAAGCACTGAACTGCTGACGGTCCCTGTGGTGACTT[A/G]
AAAGAGGTAACACTGTTTGGCGCAGTATTGCCACTAGGGGCACGCTGCTGTGGCTGAGGTGCCGGATGGTTCATCTGAGGACGAGGGGCGTAGCCTGGCT
AGCCAGGCTACGCCCCTCGTCCTCAGATGAACCATCCGGCACCTCAGCCACAGCAGCGTGCCCCTAGTGGCAATACTGCGCCAAACAGTGTTACCTCTTT[T/C]
AAGTCACCACAGGGACCGTCAGCAGTTCAGTGCTTCCGGTGCAACCAGATGGGTCACTATGCCAGACAGTGTCCTCAGAATCCTACCAACACCAACTCAG
| 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 | 36.30% | 1.80% | 21.39% | 40.52% | NA |
| All Indica | 2759 | 3.70% | 1.20% | 28.16% | 66.98% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.26% | 2.51% | NA |
| Aus | 269 | 6.30% | 18.20% | 75.46% | 0.00% | NA |
| Indica I | 595 | 2.20% | 1.20% | 6.72% | 89.92% | NA |
| Indica II | 465 | 3.90% | 0.00% | 16.13% | 80.00% | NA |
| Indica III | 913 | 2.70% | 1.20% | 46.22% | 49.84% | NA |
| Indica Intermediate | 786 | 5.70% | 1.90% | 30.53% | 61.83% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 97.20% | 0.00% | 0.60% | 2.18% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 0.00% | 6.22% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 8.33% | 3.12% | NA |
| Intermediate | 90 | 48.90% | 1.10% | 21.11% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802222500 | A -> G | LOC_Os08g04510.1 | synonymous_variant ; p.Phe556Phe; LOW | synonymous_codon | Average:23.386; most accessible tissue: Zhenshan97 young leaf, score: 43.913 | N | N | N | N |
| vg0802222500 | A -> DEL | LOC_Os08g04510.1 | N | frameshift_variant | Average:23.386; most accessible tissue: Zhenshan97 young leaf, score: 43.913 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0802222500 | NA | 6.03E-12 | mr1281 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0802222500 | 3.62E-07 | 3.62E-07 | mr1832 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |