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Detailed information for vg0332987751:

Variant ID: vg0332987751 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 32987751
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCTTCCCCGCGGCGGCGGCGGATGCAGAAGAGGAGGGCGCGACGCCGGCGACGGTCAGCTTGGCCATCGCCTTCTCCGCGGCGGCGGATGCAGAAGAG[G/A]
AGGAGGACGCGACGGCGACGCTCAGCCTGGTGTTGTTCTCGGGCCTCGCGAAGGCGAAGAAGCCTCCGTGCTCGCGCTTGGCCGTCGCCTCCCCCGCGGC

Reverse complement sequence

GCCGCGGGGGAGGCGACGGCCAAGCGCGAGCACGGAGGCTTCTTCGCCTTCGCGAGGCCCGAGAACAACACCAGGCTGAGCGTCGCCGTCGCGTCCTCCT[C/T]
CTCTTCTGCATCCGCCGCCGCGGAGAAGGCGATGGCCAAGCTGACCGTCGCCGGCGTCGCGCCCTCCTCTTCTGCATCCGCCGCCGCCGCGGGGAAGGCG

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 59.10% 40.80% 0.08% 0.02% NA
All Indica  2759 90.40% 9.50% 0.11% 0.04% NA
All Japonica  1512 0.60% 99.40% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 95.80% 4.00% 0.00% 0.17% NA
Indica II  465 92.50% 7.50% 0.00% 0.00% NA
Indica III  913 88.10% 11.70% 0.22% 0.00% NA
Indica Intermediate  786 87.80% 12.10% 0.13% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 44.40% 54.40% 1.11% 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
vg0332987751 G -> A LOC_Os03g57920.1 missense_variant ; p.Ser91Phe; MODERATE nonsynonymous_codon ; S91F Average:84.867; most accessible tissue: Minghui63 panicle, score: 92.666 unknown unknown TOLERATED 0.09
vg0332987751 G -> DEL LOC_Os03g57920.1 N frameshift_variant Average:84.867; most accessible tissue: Minghui63 panicle, score: 92.666 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)
vg0332987751 G A -0.02 -0.02 -0.03 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0332987751 NA 3.43E-17 mr1566 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
vg0332987751 NA 1.90E-10 mr1630 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
vg0332987751 8.45E-06 4.92E-38 mr1723 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
vg0332987751 NA 1.31E-07 mr1723 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
vg0332987751 NA 1.91E-39 mr1891 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
vg0332987751 NA 3.05E-43 mr1723_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
vg0332987751 NA 1.38E-08 mr1723_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