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Detailed information for vg0202763283:

Variant ID: vg0202763283 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2763283
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTTTTCGGTACTGTTTGATGATCTTGGAAAAATGCGTTAATGTTTTTTCTTTACAATAAAGGAAGCTTTATTGATATAAAACAATTAAATCAAGATGA[T/A]
ACAATAATCTTAGAACCACTTTTGACTTATGCATATCTAGAATACATATAGTCTAAAATGTTTCTGGTAAACATAATGGACACACTAATGACTATCTATC

Reverse complement sequence

GATAGATAGTCATTAGTGTGTCCATTATGTTTACCAGAAACATTTTAGACTATATGTATTCTAGATATGCATAAGTCAAAAGTGGTTCTAAGATTATTGT[A/T]
TCATCTTGATTTAATTGTTTTATATCAATAAAGCTTCCTTTATTGTAAAGAAAAAACATTAACGCATTTTTCCAAGATCATCAAACAGTACCGAAAAAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 5.10% 0.00% 0.00% NA
All Indica  2759 91.60% 8.40% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.10% 5.90% 0.00% 0.00% NA
Indica II  465 88.40% 11.60% 0.00% 0.00% NA
Indica III  913 90.80% 9.20% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.60% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 96.70% 3.30% 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
vg0202763283 T -> A LOC_Os02g05650.1 upstream_gene_variant ; 401.0bp to feature; MODIFIER silent_mutation Average:41.032; most accessible tissue: Zhenshan97 flower, score: 64.273 N N N N
vg0202763283 T -> A LOC_Os02g05640.1 downstream_gene_variant ; 4569.0bp to feature; MODIFIER silent_mutation Average:41.032; most accessible tissue: Zhenshan97 flower, score: 64.273 N N N N
vg0202763283 T -> A LOC_Os02g05660.1 downstream_gene_variant ; 2934.0bp to feature; MODIFIER silent_mutation Average:41.032; most accessible tissue: Zhenshan97 flower, score: 64.273 N N N N
vg0202763283 T -> A LOC_Os02g05650-LOC_Os02g05660 intergenic_region ; MODIFIER silent_mutation Average:41.032; most accessible tissue: Zhenshan97 flower, score: 64.273 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202763283 2.04E-06 NA mr1911_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
vg0202763283 NA 2.30E-06 mr1911_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