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Detailed information for vg0431803015:

Variant ID: vg0431803015 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31803015
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, G: 0.41, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CTGCCGAACGACTCCGGATTCGGCAAAGACGCGGCAATGCAGCGGCGTCTGCTGGTGGCTGCCGATCGCTACGGGGTGGACAGGCTGAGGGCGATGTGCG[G/A]
GGTCAAGCTGTACAAGAGCGTTAGCGTTGGGACGGTCGTGGATTCCCTGGAATTCGCAGAGAAGCACCACTGCGCGCAGCTCAAGGATGCTTGCCTTGGA

Reverse complement sequence

TCCAAGGCAAGCATCCTTGAGCTGCGCGCAGTGGTGCTTCTCTGCGAATTCCAGGGAATCCACGACCGTCCCAACGCTAACGCTCTTGTACAGCTTGACC[C/T]
CGCACATCGCCCTCAGCCTGTCCACCCCGTAGCGATCGGCAGCCACCAGCAGACGCCGCTGCATTGCCGCGTCTTTGCCGAATCCGGAGTCGTTCGGCAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.00% 26.80% 0.15% 0.00% NA
All Indica  2759 62.60% 37.20% 0.22% 0.00% NA
All Japonica  1512 93.20% 6.70% 0.07% 0.00% NA
Aus  269 62.80% 37.20% 0.00% 0.00% NA
Indica I  595 82.00% 18.00% 0.00% 0.00% NA
Indica II  465 62.20% 37.60% 0.22% 0.00% NA
Indica III  913 46.50% 53.10% 0.33% 0.00% NA
Indica Intermediate  786 66.80% 33.00% 0.25% 0.00% NA
Temperate Japonica  767 93.40% 6.50% 0.13% 0.00% NA
Tropical Japonica  504 91.70% 8.30% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0431803015 G -> A LOC_Os04g53390.1 missense_variant ; p.Gly236Glu; MODERATE nonsynonymous_codon ; G236E Average:80.753; most accessible tissue: Zhenshan97 flower, score: 94.41 benign -0.031 TOLERATED 1.00

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)
vg0431803015 G A -0.08 -0.07 -0.07 -0.06 -0.08 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431803015 5.24E-14 5.24E-14 mr1855 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
vg0431803015 7.83E-06 3.65E-06 mr1962 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