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Detailed information for vg0327580307:

Variant ID: vg0327580307 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27580307
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAAGCTGTCTAGCTTTCTTTGGCAGACTAAACTATGGAAGCAAAACAAACAAGGGCTAAGCATGTGTGGCTGACTAACATGAGGTGCGGCATTATGTG[A/G]
CATGGATCCAAACAGCCCCTGAATTCTTTTACGAAGCAAAGCTAAGCTAGAGATCTATCTCAGTTAATTATGTACATTTGGTAGCTTGTAATTAAGTTTG

Reverse complement sequence

CAAACTTAATTACAAGCTACCAAATGTACATAATTAACTGAGATAGATCTCTAGCTTAGCTTTGCTTCGTAAAAGAATTCAGGGGCTGTTTGGATCCATG[T/C]
CACATAATGCCGCACCTCATGTTAGTCAGCCACACATGCTTAGCCCTTGTTTGTTTTGCTTCCATAGTTTAGTCTGCCAAAGAAAGCTAGACAGCTTCTT

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 73.70% 19.40% 0.19% 6.75% NA
All Indica  2759 67.30% 20.90% 0.33% 11.38% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 52.80% 1.50% 1.01% 44.71% NA
Indica II  465 43.40% 54.40% 0.00% 2.15% NA
Indica III  913 89.20% 10.30% 0.11% 0.44% NA
Indica Intermediate  786 67.20% 28.20% 0.25% 4.33% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 67.80% 26.70% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0327580307 A -> DEL N N silent_mutation Average:53.015; most accessible tissue: Callus, score: 87.914 N N N N
vg0327580307 A -> G LOC_Os03g48430.1 downstream_gene_variant ; 602.0bp to feature; MODIFIER silent_mutation Average:53.015; most accessible tissue: Callus, score: 87.914 N N N N
vg0327580307 A -> G LOC_Os03g48440.1 downstream_gene_variant ; 3578.0bp to feature; MODIFIER silent_mutation Average:53.015; most accessible tissue: Callus, score: 87.914 N N N N
vg0327580307 A -> G LOC_Os03g48410-LOC_Os03g48430 intergenic_region ; MODIFIER silent_mutation Average:53.015; most accessible tissue: Callus, score: 87.914 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0327580307 5.00E-11 5.31E-20 mr1193 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
vg0327580307 1.46E-09 1.80E-14 mr1193 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
vg0327580307 NA 1.69E-11 mr1232 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
vg0327580307 NA 5.26E-07 mr1291 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
vg0327580307 NA 2.85E-19 mr1557 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
vg0327580307 NA 3.23E-07 mr1587 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
vg0327580307 NA 9.73E-06 mr1684 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
vg0327580307 NA 4.21E-06 mr1693 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
vg0327580307 NA 4.84E-10 mr1722 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
vg0327580307 NA 2.35E-07 mr1815 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
vg0327580307 8.38E-13 6.59E-27 mr1193_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
vg0327580307 3.40E-11 1.67E-12 mr1193_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
vg0327580307 NA 1.96E-16 mr1557_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
vg0327580307 NA 7.49E-08 mr1557_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
vg0327580307 NA 9.59E-06 mr1974_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