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Detailed information for vg0825087446:

Variant ID: vg0825087446 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25087446
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CTCTTTGCTTAAAACGGCCACAAAAAAACGTGGTTTTCTCTGCTCTGCCCCTCCCCTTGGGCAAGAAAACATACGCTCAGGTGTGCCCATGGGGCAATGG[G/T]
CCCTACCAATGCTTAACTTTGCTGGTTTAAAGCCACCCTCCATGGGTTTGCCTTTTGTTGTCAAGTCATCTCTTTGTCACTCCATCTTTCATAAAGCCAT

Reverse complement sequence

ATGGCTTTATGAAAGATGGAGTGACAAAGAGATGACTTGACAACAAAAGGCAAACCCATGGAGGGTGGCTTTAAACCAGCAAAGTTAAGCATTGGTAGGG[C/A]
CCATTGCCCCATGGGCACACCTGAGCGTATGTTTTCTTGCCCAAGGGGAGGGGCAGAGCAGAGAAAACCACGTTTTTTTGTGGCCGTTTTAAGCAAAGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.60% 30.90% 2.50% 0.00% NA
All Indica  2759 46.20% 50.10% 3.77% 0.00% NA
All Japonica  1512 97.40% 1.90% 0.79% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 42.40% 48.10% 9.58% 0.00% NA
Indica II  465 24.70% 72.00% 3.23% 0.00% NA
Indica III  913 61.00% 38.60% 0.44% 0.00% NA
Indica Intermediate  786 44.50% 51.90% 3.56% 0.00% NA
Temperate Japonica  767 97.80% 1.40% 0.78% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 92.10% 5.80% 2.07% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 66.70% 31.10% 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
vg0825087446 G -> T LOC_Os08g39630.1 upstream_gene_variant ; 2077.0bp to feature; MODIFIER silent_mutation Average:97.376; most accessible tissue: Zhenshan97 flower, score: 99.343 N N N N
vg0825087446 G -> T LOC_Os08g39620-LOC_Os08g39630 intergenic_region ; MODIFIER silent_mutation Average:97.376; most accessible tissue: Zhenshan97 flower, score: 99.343 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)
vg0825087446 G T -0.35 -0.37 -0.22 -0.19 -0.1 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825087446 NA 1.14E-06 mr1699 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
vg0825087446 1.07E-15 NA mr1874 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
vg0825087446 2.07E-17 2.00E-24 mr1874 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
vg0825087446 NA 5.55E-06 mr1341_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
vg0825087446 2.27E-06 NA mr1699_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
vg0825087446 1.23E-06 2.72E-09 mr1699_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
vg0825087446 1.25E-22 NA mr1874_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
vg0825087446 1.07E-22 2.41E-35 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