Search for Variation information by Variation ID:
Detailed information for vg0801237292:
| Variant ID: vg0801237292 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1237292 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 65. )
Flanking Sequence (100 bp) in Reference Genome:
CTCTTCTGTGGATCCAGTTGTGGTCCTACAACCAACTGGCAATTTATAGCCGAAGCCCTAGAATCAAAGAAACAATTTCCTTTGGGCAAAATCCTCCTCG[A/G]
CTATTTATACCAAATGTTGAACAATGCATCGGCCAAGATAGCTGTCGGATCGGTAGTTGGAGTAGGTAGACCATGGTGGTTGCTGCAGACCTGGTTAAAC
Reverse complement sequence
GTTTAACCAGGTCTGCAGCAACCACCATGGTCTACCTACTCCAACTACCGATCCGACAGCTATCTTGGCCGATGCATTGTTCAACATTTGGTATAAATAG[T/C]
CGAGGAGGATTTTGCCCAAAGGAAATTGTTTCTTTGATTCTAGGGCTTCGGCTATAAATTGCCAGTTGGTTGTAGGACCACAACTGGATCCACAGAAGAG
Allele Frequencies:
| 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 | 27.00% | 11.30% | 11.49% | 50.15% | NA |
| All Indica | 2759 | 12.20% | 10.30% | 18.63% | 58.93% | NA |
| All Japonica | 1512 | 54.60% | 0.50% | 0.40% | 44.44% | NA |
| Aus | 269 | 1.50% | 84.40% | 4.09% | 10.04% | NA |
| Indica I | 595 | 4.00% | 2.00% | 16.81% | 77.14% | NA |
| Indica II | 465 | 4.70% | 6.20% | 9.89% | 79.14% | NA |
| Indica III | 913 | 18.40% | 15.90% | 28.81% | 36.91% | NA |
| Indica Intermediate | 786 | 15.50% | 12.30% | 13.36% | 58.78% | NA |
| Temperate Japonica | 767 | 67.00% | 0.50% | 0.39% | 32.07% | NA |
| Tropical Japonica | 504 | 23.00% | 0.60% | 0.40% | 75.99% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.40% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 87.50% | 6.20% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 30.00% | 13.30% | 13.33% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801237292 | A -> G | LOC_Os08g02890.1 | missense_variant ; p.Asp248Gly; MODERATE | nonsynonymous_codon ; D248G | Average:8.237; most accessible tissue: Callus, score: 29.751 | benign  |
-0.71 |
TOLERATED | 1.00 |
| vg0801237292 | A -> DEL | LOC_Os08g02890.1 | N | frameshift_variant | Average:8.237; most accessible tissue: Callus, score: 29.751 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0801237292 | NA | 6.36E-07 | mr1342 | Jap_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 |