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Detailed information for vg0805209698:

Variant ID: vg0805209698 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5209698
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TATATCAATTGAGAAAAAAAAAAGTTTGCTTCGCTAGGATATATTTATTATGAGAAATATCAAGCAATTAACTTAATCAAAACGTAGCTACTAGTTTTAG[C/T]
TTTTCCGGCAGCATACTTTAACCCTCAACACCCTTCCATGATCACTCTTTTCTTGAAAAGAAACCTTTCACCTTTTCCCTGAGCTATTCTCTGCTCTATA

Reverse complement sequence

TATAGAGCAGAGAATAGCTCAGGGAAAAGGTGAAAGGTTTCTTTTCAAGAAAAGAGTGATCATGGAAGGGTGTTGAGGGTTAAAGTATGCTGCCGGAAAA[G/A]
CTAAAACTAGTAGCTACGTTTTGATTAAGTTAATTGCTTGATATTTCTCATAATAAATATATCCTAGCGAAGCAAACTTTTTTTTTTCTCAATTGATATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 3.80% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 88.20% 11.70% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 81.20% 18.60% 0.13% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 87.60% 12.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0805209698 C -> T LOC_Os08g08950.1 downstream_gene_variant ; 3619.0bp to feature; MODIFIER silent_mutation Average:40.986; most accessible tissue: Callus, score: 79.646 N N N N
vg0805209698 C -> T LOC_Os08g08960.1 downstream_gene_variant ; 129.0bp to feature; MODIFIER silent_mutation Average:40.986; most accessible tissue: Callus, score: 79.646 N N N N
vg0805209698 C -> T LOC_Os08g08960-LOC_Os08g08970 intergenic_region ; MODIFIER silent_mutation Average:40.986; most accessible tissue: Callus, score: 79.646 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805209698 NA 3.49E-06 mr1062 Jap_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
vg0805209698 8.98E-07 NA mr1631_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
vg0805209698 NA 4.07E-08 mr1631_2 Jap_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