| Variant ID: vg0404806507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4806507 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.04, others allele: 0.00, population size: 49. )
ATCTAAAGTGGTTTTGTCCTATGTGGTGTACACGTGGCAATCCAGTCAGCATTTTATTTTTTAAAAAATAGTGGGACCCACTTGTCATACCATATCTTCC[C/G]
CTCTTCCTTTTCCTCTCTCTCAGGCTCAGAGCGTGCACGGCGAGCGGCGGCGCGCGGGGGAGGACAGGCAGTCGGTGCGCGGGGGCCGGCGATGGGCGGT
ACCGCCCATCGCCGGCCCCCGCGCACCGACTGCCTGTCCTCCCCCGCGCGCCGCCGCTCGCCGTGCACGCTCTGAGCCTGAGAGAGAGGAAAAGGAAGAG[G/C]
GGAAGATATGGTATGACAAGTGGGTCCCACTATTTTTTAAAAAATAAAATGCTGACTGGATTGCCACGTGTACACCACATAGGACAAAACCACTTTAGAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.40% | 9.50% | 1.59% | 10.52% | NA |
| All Indica | 2759 | 79.40% | 3.70% | 1.05% | 15.80% | NA |
| All Japonica | 1512 | 73.00% | 22.30% | 2.91% | 1.79% | NA |
| Aus | 269 | 88.50% | 0.40% | 0.37% | 10.78% | NA |
| Indica I | 595 | 99.00% | 0.70% | 0.17% | 0.17% | NA |
| Indica II | 465 | 78.50% | 8.20% | 1.51% | 11.83% | NA |
| Indica III | 913 | 68.70% | 2.30% | 1.10% | 27.93% | NA |
| Indica Intermediate | 786 | 77.60% | 5.10% | 1.40% | 15.90% | NA |
| Temperate Japonica | 767 | 85.00% | 13.40% | 1.30% | 0.26% | NA |
| Tropical Japonica | 504 | 64.50% | 25.00% | 6.35% | 4.17% | NA |
| Japonica Intermediate | 241 | 52.70% | 44.80% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 8.90% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404806507 | C -> DEL | N | N | silent_mutation | Average:65.109; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | N | N | N | N |
| vg0404806507 | C -> G | LOC_Os04g08792.1 | upstream_gene_variant ; 2088.0bp to feature; MODIFIER | silent_mutation | Average:65.109; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | N | N | N | N |
| vg0404806507 | C -> G | LOC_Os04g08796.1 | upstream_gene_variant ; 4117.0bp to feature; MODIFIER | silent_mutation | Average:65.109; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | N | N | N | N |
| vg0404806507 | C -> G | LOC_Os04g08792-LOC_Os04g08796 | intergenic_region ; MODIFIER | silent_mutation | Average:65.109; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404806507 | 4.47E-07 | NA | mr1679 | 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 |
| vg0404806507 | 2.35E-07 | NA | mr1693 | 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 |
| vg0404806507 | 4.69E-06 | NA | mr1693 | Jap_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 |
| vg0404806507 | 3.18E-06 | NA | mr1720 | 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 |