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Detailed information for vg0818525912:

Variant ID: vg0818525912 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18525912
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TAACCAAGTGATAAATAATAGGTAATCAACATCAAAAGGCTATAACAAAGGCAATAGGTTATTTCCACCCAATGACATTCGAAAATAAATGCAATAGTTG[A/G]
ATAGAAACAATAGCTTTAAATGGGATCAACATGCTCAAAGGGTTGTTTGGGATCTGTGTGACTTGCCTTGCAGGCCTTGGAATCGGATTCTCCGGGAACG

Reverse complement sequence

CGTTCCCGGAGAATCCGATTCCAAGGCCTGCAAGGCAAGTCACACAGATCCCAAACAACCCTTTGAGCATGTTGATCCCATTTAAAGCTATTGTTTCTAT[T/C]
CAACTATTGCATTTATTTTCGAATGTCATTGGGTGGAAATAACCTATTGCCTTTGTTATAGCCTTTTGATGTTGATTACCTATTATTTATCACTTGGTTA

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 76.90% 21.10% 1.33% 0.74% NA
All Indica  2759 68.00% 28.60% 2.21% 1.23% NA
All Japonica  1512 87.80% 12.20% 0.07% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 71.10% 28.20% 0.67% 0.00% NA
Indica II  465 89.90% 9.90% 0.22% 0.00% NA
Indica III  913 56.00% 36.80% 4.38% 2.85% NA
Indica Intermediate  786 66.50% 30.40% 2.04% 1.02% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 68.50% 31.30% 0.20% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 83.30% 15.60% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818525912 A -> G LOC_Os08g30120-LOC_Os08g30140 intergenic_region ; MODIFIER silent_mutation Average:24.948; most accessible tissue: Zhenshan97 flower, score: 39.624 N N N N
vg0818525912 A -> DEL N N silent_mutation Average:24.948; most accessible tissue: Zhenshan97 flower, score: 39.624 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818525912 NA 3.85E-06 mr1227 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
vg0818525912 1.29E-07 1.29E-07 mr1266 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
vg0818525912 NA 9.19E-06 mr1304 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
vg0818525912 NA 1.81E-07 mr1345 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
vg0818525912 3.58E-06 3.58E-06 mr1356 Jap_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
vg0818525912 2.70E-06 5.90E-08 mr1427 Jap_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
vg0818525912 9.07E-07 2.77E-08 mr1622 Jap_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
vg0818525912 NA 5.38E-07 mr1638 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
vg0818525912 NA 4.81E-06 mr1700 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
vg0818525912 NA 1.48E-06 mr1866 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