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Detailed information for vg0308314268:

Variant ID: vg0308314268 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8314268
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, T: 0.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TACGCAAACAAACAAAAACCTAAACAAAAGACCAAGAAAAAGACCCTATTTAGACTGAATAATAGTGCCATTAAATAGATCTCAATTTTACGGAATTACT[A/G]
GAAGTTGAACGGAGTCAATCGGAAGAGCGGTTGGGAAGATATGAATTTTGGAAGTTTAATTGGAATTTCTGGAAGACGAGAAATGGTTTATGGAATTTAT

Reverse complement sequence

ATAAATTCCATAAACCATTTCTCGTCTTCCAGAAATTCCAATTAAACTTCCAAAATTCATATCTTCCCAACCGCTCTTCCGATTGACTCCGTTCAACTTC[T/C]
AGTAATTCCGTAAAATTGAGATCTATTTAATGGCACTATTATTCAGTCTAAATAGGGTCTTTTTCTTGGTCTTTTGTTTAGGTTTTTGTTTGTTTGCGTA

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 91.30% 8.10% 0.51% 0.00% NA
All Indica  2759 97.40% 1.80% 0.83% 0.00% NA
All Japonica  1512 79.20% 20.80% 0.07% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 98.20% 0.80% 1.01% 0.00% NA
Indica II  465 97.80% 1.50% 0.65% 0.00% NA
Indica III  913 96.50% 2.60% 0.88% 0.00% NA
Indica Intermediate  786 97.50% 1.80% 0.76% 0.00% NA
Temperate Japonica  767 61.00% 38.90% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0308314268 A -> G LOC_Os03g15190.1 upstream_gene_variant ; 2711.0bp to feature; MODIFIER silent_mutation Average:10.153; most accessible tissue: Zhenshan97 root, score: 16.934 N N N N
vg0308314268 A -> G LOC_Os03g15190-LOC_Os03g15200 intergenic_region ; MODIFIER silent_mutation Average:10.153; most accessible tissue: Zhenshan97 root, score: 16.934 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308314268 NA 9.39E-07 mr1026 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
vg0308314268 NA 8.09E-07 mr1171 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
vg0308314268 NA 5.19E-06 mr1328 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
vg0308314268 6.30E-07 NA mr1585 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
vg0308314268 NA 1.16E-07 mr1585 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
vg0308314268 NA 1.62E-14 mr1712 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
vg0308314268 NA 1.23E-06 mr1712 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
vg0308314268 1.52E-06 1.52E-06 mr1779 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
vg0308314268 NA 1.17E-08 mr1946 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
vg0308314268 NA 2.40E-08 mr1977 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
vg0308314268 NA 5.84E-06 mr1977 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