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Detailed information for vg0314909213:

Variant ID: vg0314909213 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14909213
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAAAAACCTTGTGTATTAGTAGATTGAACAGCCAATTCAGTCAGCAAAGTTTGAGCAGCAGGATCCACTGAATAAGAATTTAACACCTCCTGGAGCCA[G/A]
AGGGGAGAAGCCACTGACAGTGCAGCACAATGAGGTATAACAGGCATCCTGGACAGCGCATCAGCAACTATATTGTCAACTCCTTTTTTGTATTGAAAAG

Reverse complement sequence

CTTTTCAATACAAAAAAGGAGTTGACAATATAGTTGCTGATGCGCTGTCCAGGATGCCTGTTATACCTCATTGTGCTGCACTGTCAGTGGCTTCTCCCCT[C/T]
TGGCTCCAGGAGGTGTTAAATTCTTATTCAGTGGATCCTGCTGCTCAAACTTTGCTGACTGAATTGGCTGTTCAATCTACTAATACACAAGGTTTTTCTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.10% 20.80% 0.13% 0.00% NA
All Indica  2759 68.30% 31.50% 0.18% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 67.30% 32.70% 0.00% 0.00% NA
Indica I  595 42.50% 57.30% 0.17% 0.00% NA
Indica II  465 58.10% 41.70% 0.22% 0.00% NA
Indica III  913 85.80% 13.90% 0.33% 0.00% NA
Indica Intermediate  786 73.50% 26.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0314909213 G -> A LOC_Os03g26010.1 upstream_gene_variant ; 253.0bp to feature; MODIFIER silent_mutation Average:31.274; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0314909213 G -> A LOC_Os03g26000.1 downstream_gene_variant ; 2240.0bp to feature; MODIFIER silent_mutation Average:31.274; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0314909213 G -> A LOC_Os03g26020.1 downstream_gene_variant ; 216.0bp to feature; MODIFIER silent_mutation Average:31.274; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0314909213 G -> A LOC_Os03g26010-LOC_Os03g26020 intergenic_region ; MODIFIER silent_mutation Average:31.274; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314909213 7.79E-06 7.79E-06 mr1337 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
vg0314909213 NA 6.85E-07 mr1376 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
vg0314909213 NA 6.85E-07 mr1431 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
vg0314909213 3.11E-08 2.02E-08 mr1484 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
vg0314909213 NA 7.99E-06 mr1500 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
vg0314909213 NA 2.50E-06 mr1500 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
vg0314909213 1.33E-06 5.02E-07 mr1505 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
vg0314909213 1.49E-07 NA mr1542 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
vg0314909213 1.97E-06 1.04E-07 mr1542 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
vg0314909213 NA 5.48E-06 mr1956 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
vg0314909213 NA 9.41E-07 mr1959 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
vg0314909213 4.14E-06 NA mr1542_2 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
vg0314909213 NA 1.86E-08 mr1542_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