Search for Variation information by Variation ID:
Detailed information for vg0809308950:
| Variant ID: vg0809308950 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9308950 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.85, C: 0.16, others allele: 0.00, population size: 113. )
Flanking Sequence (100 bp) in Reference Genome:
TTCAGCTATCTCTTTTGGATTCTTGCCCTTCAGCTGGTCAGACCCTGGTGCTAACCTCACGGTATGCTGTGTTTGGCAGATCCGAGTTGGATCCAAGAAG[T/C]
CGATAGGTTCTTTTTTCTTCTTAGCATCCATGTATTGCATCCTACAGAAGAAGTTTGTTAGTAACAATTACATGGATTTGTATTGTACATATTTTTCATA
Reverse complement sequence
TATGAAAAATATGTACAATACAAATCCATGTAATTGTTACTAACAAACTTCTTCTGTAGGATGCAATACATGGATGCTAAGAAGAAAAAAGAACCTATCG[A/G]
CTTCTTGGATCCAACTCGGATCTGCCAAACACAGCATACCGTGAGGTTAGCACCAGGGTCTGACCAGCTGAAGGGCAAGAATCCAAAAGAGATAGCTGAA
Allele Frequencies:
| 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 | 52.60% | 47.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 75.30% | 24.60% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 6.30% | 93.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 68.70% | 31.10% | 0.17% | 0.00% | NA |
| Indica II | 465 | 48.20% | 51.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 74.30% | 25.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 12.30% | 87.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 41.10% | 58.90% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809308950 | T -> C | LOC_Os08g15310.1 | missense_variant ; p.Asp453Gly; MODERATE | nonsynonymous_codon ; D453G | Average:29.496; most accessible tissue: Callus, score: 51.279 | probably damaging  |
-2.142 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809308950 | NA | 2.71E-18 | mr1133 | 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 |
| vg0809308950 | NA | 5.24E-18 | mr1162_2 | 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 |
| vg0809308950 | NA | 9.80E-06 | mr1452_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 |
| vg0809308950 | NA | 3.50E-06 | mr1582_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 |