| Variant ID: vg0817248199 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17248199 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 204. )
ATAACAGTAACTTCAATCAGCCCTCCGTGAAGGACTTAGTTTTTGCGCAGGCTAAAACAAATGATGCTATAAACAAAAAGCTTGCCTTGAATGTTAAAGT[T/A]
CTTGAGAATATAAATGTCAAGCTAGAAGGCTTTGCTTCCGCTTTCCAAAACCAGCTGAGCTTCAACAAAATGATAGACTCTGCTGGTGCAACTAGACTCT
AGAGTCTAGTTGCACCAGCAGAGTCTATCATTTTGTTGAAGCTCAGCTGGTTTTGGAAAGCGGAAGCAAAGCCTTCTAGCTTGACATTTATATTCTCAAG[A/T]
ACTTTAACATTCAAGGCAAGCTTTTTGTTTATAGCATCATTTGTTTTAGCCTGCGCAAAAACTAAGTCCTTCACGGAGGGCTGATTGAAGTTACTGTTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.50% | 25.00% | 2.43% | 27.08% | NA |
| All Indica | 2759 | 15.70% | 41.60% | 3.33% | 39.40% | NA |
| All Japonica | 1512 | 93.40% | 0.30% | 0.07% | 6.22% | NA |
| Aus | 269 | 59.10% | 7.40% | 7.06% | 26.39% | NA |
| Indica I | 595 | 10.80% | 53.40% | 1.51% | 34.29% | NA |
| Indica II | 465 | 8.20% | 65.60% | 2.80% | 23.44% | NA |
| Indica III | 913 | 25.00% | 22.10% | 3.83% | 49.07% | NA |
| Indica Intermediate | 786 | 13.00% | 41.10% | 4.45% | 41.48% | NA |
| Temperate Japonica | 767 | 99.00% | 0.10% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 83.90% | 0.40% | 0.20% | 15.48% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.80% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 64.40% | 10.00% | 3.33% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817248199 | T -> A | LOC_Os08g28260.1 | synonymous_variant ; p.Val276Val; LOW | synonymous_codon | Average:25.344; most accessible tissue: Callus, score: 59.456 | N | N | N | N |
| vg0817248199 | T -> DEL | LOC_Os08g28260.1 | N | frameshift_variant | Average:25.344; most accessible tissue: Callus, score: 59.456 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817248199 | 1.12E-06 | NA | mr1746 | 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 |
| vg0817248199 | 4.50E-07 | 2.32E-06 | mr1746 | 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 |