| Variant ID: vg0819371692 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19371692 |
| Reference Allele: T | Alternative Allele: C,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 263. )
TGGAAACTTTCATCTAGGTCATGGCGAGGGAGGTTTTAAAGGTGCTCGAGGCTGGTTTGGCAGAAATCGCTTTGGAGCTCGGAATTTTGCTGGAGGCCGG[T/C,A]
AGGGGCAAGGTGGAAGAGGTTGGAACATCAATGGTGGATGGCAACCAAATGTTGGTTCCCATGGCGGAGAAGATGGCCGGTTTGGACAGGAGAATTTTAG
CTAAAATTCTCCTGTCCAAACCGGCCATCTTCTCCGCCATGGGAACCAACATTTGGTTGCCATCCACCATTGATGTTCCAACCTCTTCCACCTTGCCCCT[A/G,T]
CCGGCCTCCAGCAAAATTCCGAGCTCCAAAGCGATTTCTGCCAAACCAGCCTCGAGCACCTTTAAAACCTCCCTCGCCATGACCTAGATGAAAGTTTCCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.60% | 35.30% | 1.90% | 0.00% | A: 0.17% |
| All Indica | 2759 | 84.10% | 13.40% | 2.43% | 0.00% | NA |
| All Japonica | 1512 | 18.70% | 79.40% | 1.39% | 0.00% | A: 0.53% |
| Aus | 269 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.80% | 4.90% | 2.35% | 0.00% | NA |
| Indica II | 465 | 95.50% | 3.40% | 1.08% | 0.00% | NA |
| Indica III | 913 | 78.40% | 21.00% | 0.55% | 0.00% | NA |
| Indica Intermediate | 786 | 77.50% | 17.00% | 5.47% | 0.00% | NA |
| Temperate Japonica | 767 | 6.60% | 92.60% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 37.10% | 58.90% | 2.38% | 0.00% | A: 1.59% |
| Japonica Intermediate | 241 | 18.70% | 80.10% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 52.10% | 47.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 47.80% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819371692 | T -> C | LOC_Os08g31320.1 | synonymous_variant ; p.Gly27Gly; LOW | synonymous_codon | Average:48.832; most accessible tissue: Zhenshan97 young leaf, score: 66.32 | N | N | N | N |
| vg0819371692 | T -> A | LOC_Os08g31320.1 | synonymous_variant ; p.Gly27Gly; LOW | synonymous_codon | Average:48.832; most accessible tissue: Zhenshan97 young leaf, score: 66.32 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819371692 | 3.54E-06 | 7.09E-08 | mr1164_2 | 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 |
| vg0819371692 | NA | 4.87E-06 | mr1454_2 | Ind_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 |