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Detailed information for vg0304625462:

Variant ID: vg0304625462 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 4625462
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GTATAATATACTAGTACCGGTATATACTAGCAGTATAAATTAATAAAGGCAATGTTGAAAATTTGATAGAAAATTTTATACGATAATTTTTGTAATTTGC[G/T]
GTTCAGATTTAATCTAATTGTAAATGCCCAGTCCTAGTTCTCTCGTGTATTAATATAACCATATGAAAGTATTTTGTGACAACTGTATTAATTAATTCTA

Reverse complement sequence

TAGAATTAATTAATACAGTTGTCACAAAATACTTTCATATGGTTATATTAATACACGAGAGAACTAGGACTGGGCATTTACAATTAGATTAAATCTGAAC[C/A]
GCAAATTACAAAAATTATCGTATAAAATTTTCTATCAAATTTTCAACATTGCCTTTATTAATTTATACTGCTAGTATATACCGGTACTAGTATATTATAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.20% 8.80% 0.04% 0.00% NA
All Indica  2759 85.00% 14.90% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.20% 10.80% 0.00% 0.00% NA
Indica II  465 84.10% 15.90% 0.00% 0.00% NA
Indica III  913 80.50% 19.50% 0.00% 0.00% NA
Indica Intermediate  786 87.50% 12.20% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0304625462 G -> T LOC_Os03g08930.1 upstream_gene_variant ; 3473.0bp to feature; MODIFIER silent_mutation Average:40.367; most accessible tissue: Callus, score: 65.204 N N N N
vg0304625462 G -> T LOC_Os03g08920-LOC_Os03g08930 intergenic_region ; MODIFIER silent_mutation Average:40.367; most accessible tissue: Callus, score: 65.204 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304625462 1.82E-06 5.04E-07 mr1739 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