Search for Variation information by Variation ID:
Detailed information for vg0306688786:
| Variant ID: vg0306688786 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 6688786 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.51, T: 0.49, others allele: 0.00, population size: 78. )
Flanking Sequence (100 bp) in Reference Genome:
AACAAGAGTTTGGAGAGATGCTTCAAGGGTAAGAACACTCTTGACAAGATTTTGAGTGAGCAACAGTGCATCCTTAACAAAGAGGGACTTGGATTCATTC[T/C]
AAAGAAGGGTAAGAAACCTTCTCACCGTGCCACTCGTTTTGTCAAGAGCAATGGTAAGTATTGCTCCAAGTGTCGTGAGGTTGGGCATTTGGTGAGTGAT
Reverse complement sequence
ATCACTCACCAAATGCCCAACCTCACGACACTTGGAGCAATACTTACCATTGCTCTTGACAAAACGAGTGGCACGGTGAGAAGGTTTCTTACCCTTCTTT[A/G]
GAATGAATCCAAGTCCCTCTTTGTTAAGGATGCACTGTTGCTCACTCAAAATCTTGTCAAGAGTGTTCTTACCCTTGAAGCATCTCTCCAAACTCTTGTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.00% | 1.40% | 37.54% | 18.05% | NA |
| All Indica | 2759 | 9.50% | 2.00% | 58.14% | 30.30% | NA |
| All Japonica | 1512 | 96.40% | 0.00% | 3.31% | 0.26% | NA |
| Aus | 269 | 87.00% | 3.70% | 8.92% | 0.37% | NA |
| Indica I | 595 | 3.70% | 3.00% | 53.11% | 40.17% | NA |
| Indica II | 465 | 4.30% | 2.20% | 34.41% | 59.14% | NA |
| Indica III | 913 | 13.10% | 0.70% | 75.68% | 10.51% | NA |
| Indica Intermediate | 786 | 12.80% | 2.80% | 55.60% | 28.75% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 2.48% | 0.39% | NA |
| Tropical Japonica | 504 | 94.20% | 0.00% | 5.75% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 31.20% | 2.10% | 66.67% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 35.56% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0306688786 | T -> C | LOC_Os03g12600.1 | missense_variant ; p.Leu518Pro; MODERATE | nonsynonymous_codon ; L518P | Average:17.662; most accessible tissue: Zhenshan97 root, score: 27.411 | benign  |
-1.489 |
TOLERATED | 0.58 |
| vg0306688786 | T -> DEL | LOC_Os03g12600.1 | N | frameshift_variant | Average:17.662; most accessible tissue: Zhenshan97 root, score: 27.411 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0306688786 | NA | 5.54E-43 | mr1136 | 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 |
| vg0306688786 | 6.51E-07 | 3.15E-06 | mr1720 | 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 |
| vg0306688786 | NA | 1.95E-22 | mr1888 | 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 |
| vg0306688786 | NA | 8.26E-18 | mr1682_2 | 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 |