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Detailed information for vg0220740382:

Variant ID: vg0220740382 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20740382
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGCATCGTCATGCTGCGACCCAATTCCTTGATCTACACCAACGCCCGTCTCAACTGCGACGATAGCATTATCGTCAACACACATCGGATCTCCACCCC[C/T]
GCCTTCACAGCCACCTTCACCGTCAGTGTTCACCATCACTGCAAAACCCCGAGATAATTGGGATCAATGTGTCAAAGCCACATCATAAGGCAAGTGTAAC

Reverse complement sequence

GTTACACTTGCCTTATGATGTGGCTTTGACACATTGATCCCAATTATCTCGGGGTTTTGCAGTGATGGTGAACACTGACGGTGAAGGTGGCTGTGAAGGC[G/A]
GGGGTGGAGATCCGATGTGTGTTGACGATAATGCTATCGTCGCAGTTGAGACGGGCGTTGGTGTAGATCAAGGAATTGGGTCGCAGCATGACGATGCTGG

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 90.90% 9.10% 0.00% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 75.70% 24.30% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 73.50% 26.50% 0.00% 0.00% NA
Tropical Japonica  504 79.80% 20.20% 0.00% 0.00% NA
Japonica Intermediate  241 74.30% 25.70% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0220740382 C -> T LOC_Os02g34590.1 missense_variant ; p.Gly13Arg; MODERATE nonsynonymous_codon ; G13R Average:78.638; most accessible tissue: Zhenshan97 flower, score: 88.465 unknown unknown DELETERIOUS 0.01

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)
vg0220740382 C T -0.03 -0.04 -0.04 -0.03 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220740382 8.76E-07 NA Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652