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Detailed information for vg0818530563:

Variant ID: vg0818530563 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18530563
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


GCAGGGAGTCTTGGATTTGGAGCACACCTAGGGAGGGAGGACTGGAGAATGGTTCATGTGTAGGAATAAGTCTTGGCTGGTTGGTCCTGGTCTTGTGGTG[T/C]
CTTTTCTTGCTTTTTAGCTTTCTAGGACAGCATCTCTACTTTCAGTTTGGATGCTCTAGGACAGCTAGGACAGCAGTTTGTTGAGATGCTCTAGGACAGT

Reverse complement sequence

ACTGTCCTAGAGCATCTCAACAAACTGCTGTCCTAGCTGTCCTAGAGCATCCAAACTGAAAGTAGAGATGCTGTCCTAGAAAGCTAAAAAGCAAGAAAAG[A/G]
CACCACAAGACCAGGACCAACCAGCCAAGACTTATTCCTACACATGAACCATTCTCCAGTCCTCCCTCCCTAGGTGTGCTCCAAATCCAAGACTCCCTGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 38.70% 0.49% 0.00% NA
All Indica  2759 61.90% 37.70% 0.36% 0.00% NA
All Japonica  1512 50.70% 48.90% 0.46% 0.00% NA
Aus  269 91.10% 7.40% 1.49% 0.00% NA
Indica I  595 54.80% 44.50% 0.67% 0.00% NA
Indica II  465 84.50% 15.30% 0.22% 0.00% NA
Indica III  913 58.10% 41.80% 0.11% 0.00% NA
Indica Intermediate  786 58.50% 41.00% 0.51% 0.00% NA
Temperate Japonica  767 31.20% 68.20% 0.65% 0.00% NA
Tropical Japonica  504 67.30% 32.70% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 21.20% 0.83% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 65.60% 32.20% 2.22% 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
vg0818530563 T -> C LOC_Os08g30120-LOC_Os08g30140 intergenic_region ; MODIFIER silent_mutation Average:82.23; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0818530563 T C -0.02 -0.02 -0.02 0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818530563 NA 4.75E-06 mr1164 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
vg0818530563 9.48E-07 NA mr1959_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