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Detailed information for vg0208367927:

Variant ID: vg0208367927 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8367927
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.04, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GACGGCGACCCAGAGCGCCAGGAAGAGGGAGAGCACGACGAGGGACCCCGCGTCGCCGCCCGTCCGCGACACCTGCACGATCCCGTAGACGATCATCGCC[G/C]
CGCCGCCGATGCACACGCCGTTGGCGATCGCCAGCATGTAGCACCGCACGAACCAATCCATGGCGCGCCGCCCCGGCCGCCCGCCGCCGTACGTCGACGA

Reverse complement sequence

TCGTCGACGTACGGCGGCGGGCGGCCGGGGCGGCGCGCCATGGATTGGTTCGTGCGGTGCTACATGCTGGCGATCGCCAACGGCGTGTGCATCGGCGGCG[C/G]
GGCGATGATCGTCTACGGGATCGTGCAGGTGTCGCGGACGGGCGGCGACGCGGGGTCCCTCGTCGTGCTCTCCCTCTTCCTGGCGCTCTGGGTCGCCGTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.70% 30.20% 0.11% 0.00% NA
All Indica  2759 52.60% 47.20% 0.18% 0.00% NA
All Japonica  1512 98.00% 2.00% 0.00% 0.00% NA
Aus  269 73.20% 26.80% 0.00% 0.00% NA
Indica I  595 61.80% 38.00% 0.17% 0.00% NA
Indica II  465 42.60% 57.00% 0.43% 0.00% NA
Indica III  913 46.70% 53.20% 0.11% 0.00% NA
Indica Intermediate  786 58.50% 41.30% 0.13% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0208367927 G -> C LOC_Os02g15000.1 missense_variant ; p.Ala21Gly; MODERATE nonsynonymous_codon ; A21G Average:93.785; most accessible tissue: Zhenshan97 flag leaf, score: 98.271 unknown unknown DELETERIOUS 0.02

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)
vg0208367927 G C -0.01 -0.01 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208367927 NA 8.15E-06 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