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Detailed information for vg0313073263:

Variant ID: vg0313073263 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13073263
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


TAGTTGAATATCTATTATATTATTAAAGGAATAGAAAAAGGAGCCTCCACATTCGCTCACATGGCCTAGAAATTTTCACATTAATCGGGAAAAAAGAAAA[A/G]
ACAGAGTCCATATAGAAATACAATTTAGAAATAGCAGAAATTCGAAATTAAAAAATAAGGAATATTAGAAAAGGAGACTAGAGTCCATATAGAAATACAA

Reverse complement sequence

TTGTATTTCTATATGGACTCTAGTCTCCTTTTCTAATATTCCTTATTTTTTAATTTCGAATTTCTGCTATTTCTAAATTGTATTTCTATATGGACTCTGT[T/C]
TTTTCTTTTTTCCCGATTAATGTGAAAATTTCTAGGCCATGTGAGCGAATGTGGAGGCTCCTTTTTCTATTCCTTTAATAATATAATAGATATTCAACTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.30% 10.60% 0.06% 0.00% NA
All Indica  2759 87.10% 12.80% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 50.20% 49.80% 0.00% 0.00% NA
Indica I  595 92.10% 7.90% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 80.90% 18.90% 0.11% 0.00% NA
Indica Intermediate  786 86.90% 13.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 1.11% 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
vg0313073263 A -> G LOC_Os03g22634.1 upstream_gene_variant ; 1790.0bp to feature; MODIFIER silent_mutation Average:20.923; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0313073263 A -> G LOC_Os03g22634-LOC_Os03g22650 intergenic_region ; MODIFIER silent_mutation Average:20.923; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313073263 NA 2.29E-07 mr1004 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
vg0313073263 6.95E-06 6.96E-06 mr1275 Ind_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
vg0313073263 4.42E-07 4.42E-07 mr1302 Ind_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
vg0313073263 NA 1.02E-07 mr1762 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
vg0313073263 3.69E-06 3.69E-06 mr1762 Ind_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