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Detailed information for vg0825015850:

Variant ID: vg0825015850 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25015850
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTTTCAAATTGGGCCAAGTACCCAAGCGCACAAATATGAAACCACAACCTCTCATACAAGATCTTTAGCATTTCTTATGCTTTTGTCACTTGTACAAT[A/G]
CAAACTTTAAAGTAGAACTATCAAGTAAATCACTAGCAAAAAAGGTTAAAAGTATAAAGAAGAGAAAGGCAGGAAAGAGAAAACATTCTTCTTTTCCTTA

Reverse complement sequence

TAAGGAAAAGAAGAATGTTTTCTCTTTCCTGCCTTTCTCTTCTTTATACTTTTAACCTTTTTTGCTAGTGATTTACTTGATAGTTCTACTTTAAAGTTTG[T/C]
ATTGTACAAGTGACAAAAGCATAAGAAATGCTAAAGATCTTGTATGAGAGGTTGTGGTTTCATATTTGTGCGCTTGGGTACTTGGCCCAATTTGAAAGGT

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 89.50% 10.20% 0.17% 0.11% NA
All Indica  2759 82.30% 17.20% 0.29% 0.18% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 67.90% 31.30% 0.50% 0.34% NA
Indica II  465 91.80% 7.70% 0.22% 0.22% NA
Indica III  913 83.90% 15.90% 0.22% 0.00% NA
Indica Intermediate  786 85.90% 13.60% 0.25% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0825015850 A -> G LOC_Os08g39550.1 3_prime_UTR_variant ; 326.0bp to feature; MODIFIER silent_mutation Average:65.592; most accessible tissue: Zhenshan97 flower, score: 78.853 N N N N
vg0825015850 A -> G LOC_Os08g39540.1 downstream_gene_variant ; 2418.0bp to feature; MODIFIER silent_mutation Average:65.592; most accessible tissue: Zhenshan97 flower, score: 78.853 N N N N
vg0825015850 A -> DEL N N silent_mutation Average:65.592; most accessible tissue: Zhenshan97 flower, score: 78.853 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825015850 1.99E-15 1.97E-22 mr1874 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
vg0825015850 2.32E-15 1.81E-20 mr1874 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
vg0825015850 NA 7.40E-10 mr1709_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
vg0825015850 1.78E-17 1.51E-23 mr1874_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
vg0825015850 9.56E-17 3.78E-21 mr1874_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