| Variant ID: vg0804146568 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4146568 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.09, others allele: 0.00, population size: 86. )
TCCCTAAATATTTGACACCGTTGACTTTTTTAAACATATTTGATCGTTCATTTTATTCAAAAACTTTTGTGAATGTGTAAAACTATATGTATACATAAAA[A/G]
TATATTTAACAATAAATCAAATGATATGAAAAAAATTAATAATTACTTAAATTTTTTGAATAAGACGAACGGTCAAACATTTTTAAAAAAATCAATGGCG
CGCCATTGATTTTTTTAAAAATGTTTGACCGTTCGTCTTATTCAAAAAATTTAAGTAATTATTAATTTTTTTCATATCATTTGATTTATTGTTAAATATA[T/C]
TTTTATGTATACATATAGTTTTACACATTCACAAAAGTTTTTGAATAAAATGAACGATCAAATATGTTTAAAAAAGTCAACGGTGTCAAATATTTAGGGA
| 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 | 48.80% | 0.60% | 7.43% | 43.10% | NA |
| All Indica | 2759 | 28.90% | 0.50% | 4.13% | 66.44% | NA |
| All Japonica | 1512 | 94.80% | 0.10% | 3.57% | 1.46% | NA |
| Aus | 269 | 4.80% | 1.90% | 45.72% | 47.58% | NA |
| Indica I | 595 | 14.30% | 0.80% | 3.70% | 81.18% | NA |
| Indica II | 465 | 72.50% | 0.20% | 0.65% | 26.67% | NA |
| Indica III | 913 | 14.70% | 0.40% | 4.38% | 80.50% | NA |
| Indica Intermediate | 786 | 30.80% | 0.50% | 6.23% | 62.47% | NA |
| Temperate Japonica | 767 | 97.10% | 0.30% | 0.52% | 2.09% | NA |
| Tropical Japonica | 504 | 89.50% | 0.00% | 9.72% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 13.50% | 7.30% | 53.12% | 26.04% | NA |
| Intermediate | 90 | 55.60% | 2.20% | 10.00% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804146568 | A -> G | LOC_Os08g07380.1 | upstream_gene_variant ; 3007.0bp to feature; MODIFIER | silent_mutation | Average:47.61; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| vg0804146568 | A -> G | LOC_Os08g07390.1 | downstream_gene_variant ; 480.0bp to feature; MODIFIER | silent_mutation | Average:47.61; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| vg0804146568 | A -> G | LOC_Os08g07380-LOC_Os08g07390 | intergenic_region ; MODIFIER | silent_mutation | Average:47.61; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| vg0804146568 | A -> DEL | N | N | silent_mutation | Average:47.61; most accessible tissue: Minghui63 root, score: 76.425 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804146568 | NA | 7.51E-06 | mr1038 | 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 |
| vg0804146568 | NA | 1.80E-06 | mr1347 | 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 |
| vg0804146568 | 2.98E-06 | 3.69E-08 | mr1347 | 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 |