Search for Variation information by Variation ID:
Detailed information for vg0816083596:
| Variant ID: vg0816083596 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16083596 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 63. )
Flanking Sequence (100 bp) in Reference Genome:
GTATTCTCGCGTGTGAGCATACTCCCGGTCACTCAGCATGTAGTAGGCTTGTCTCTCCCGATCACTGACAAGGTCGAGGTCGGTGTCGTTCAGGAGTCGT[T/C]
GCGGAGCTTCGGCGTCTTCCATCGAGACATTAGCTGATGAATGAGCGCTAGACTCATCATGATGACTTAATGAAGAGCCATACCCCTTGAATAGATGAGA
Reverse complement sequence
TCTCATCTATTCAAGGGGTATGGCTCTTCATTAAGTCATCATGATGAGTCTAGCGCTCATTCATCAGCTAATGTCTCGATGGAAGACGCCGAAGCTCCGC[A/G]
ACGACTCCTGAACGACACCGACCTCGACCTTGTCAGTGATCGGGAGAGACAAGCCTACTACATGCTGAGTGACCGGGAGTATGCTCACACGCGAGAATAC
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 | 67.10% | 24.20% | 8.13% | 0.59% | NA |
| All Indica | 2759 | 93.30% | 3.40% | 3.23% | 0.07% | NA |
| All Japonica | 1512 | 20.00% | 60.60% | 17.92% | 1.39% | NA |
| Aus | 269 | 91.10% | 2.60% | 6.32% | 0.00% | NA |
| Indica I | 595 | 87.40% | 5.50% | 6.89% | 0.17% | NA |
| Indica II | 465 | 95.10% | 2.80% | 2.15% | 0.00% | NA |
| Indica III | 913 | 97.20% | 1.80% | 1.10% | 0.00% | NA |
| Indica Intermediate | 786 | 92.10% | 4.20% | 3.56% | 0.13% | NA |
| Temperate Japonica | 767 | 1.30% | 94.80% | 2.48% | 1.43% | NA |
| Tropical Japonica | 504 | 48.60% | 18.10% | 32.54% | 0.79% | NA |
| Japonica Intermediate | 241 | 19.90% | 41.10% | 36.51% | 2.49% | NA |
| VI/Aromatic | 96 | 6.20% | 89.60% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 50.00% | 41.10% | 6.67% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816083596 | T -> C | LOC_Os08g26390.1 | missense_variant ; p.Gln39Arg; MODERATE | nonsynonymous_codon ; Q39R | Average:11.216; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
-0.749 |
TOLERATED | 1.00 |
| vg0816083596 | T -> DEL | LOC_Os08g26390.1 | N | frameshift_variant | Average:11.216; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816083596 | 4.33E-06 | NA | mr1167_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 |
| vg0816083596 | NA | 7.50E-06 | mr1950_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 |