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Detailed information for vg0917594974:

Variant ID: vg0917594974 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 17594974
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGATAAATAAAAGTGGGGAGTGTTGGCTCTCATGCAAGAGTTAACTGCACACAAACTCCAAGAAATATGCATTAAATTCATGGTGAGAGAAAGAGAGG[G/T]
GATGAAGAAAATAAAGATAACCTTATAGCCAACCTACTATACATGTTAGCTTTAACATTGACTAATAGTAAGTAGTGAGCTCTACTATTAAACTTGCTCT

Reverse complement sequence

AGAGCAAGTTTAATAGTAGAGCTCACTACTTACTATTAGTCAATGTTAAAGCTAACATGTATAGTAGGTTGGCTATAAGGTTATCTTTATTTTCTTCATC[C/A]
CCTCTCTTTCTCTCACCATGAATTTAATGCATATTTCTTGGAGTTTGTGTGCAGTTAACTCTTGCATGAGAGCCAACACTCCCCACTTTTATTTATCTCT

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 54.00% 45.80% 0.19% 0.00% NA
All Indica  2759 22.10% 77.60% 0.33% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 53.90% 45.90% 0.17% 0.00% NA
Indica II  465 8.60% 91.40% 0.00% 0.00% NA
Indica III  913 2.80% 97.20% 0.00% 0.00% NA
Indica Intermediate  786 28.40% 70.60% 1.02% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg0917594974 G -> T LOC_Os09g28930-LOC_Os09g28940 intergenic_region ; MODIFIER silent_mutation Average:43.152; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0917594974 4.48E-06 NA mr1232_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
vg0917594974 3.50E-06 NA mr1557_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
vg0917594974 NA 5.03E-06 mr1603_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
vg0917594974 3.47E-06 1.99E-06 mr1603_2 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
vg0917594974 5.53E-06 NA mr1608_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
vg0917594974 6.49E-06 NA mr1608_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
vg0917594974 NA 2.96E-06 mr1942_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