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Detailed information for vg0225028520:

Variant ID: vg0225028520 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25028520
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGCAATGGGTACATTAAATAAGGTCATTGTGGTCATTTTCTAATCCTACTGTTTGGTCCTAAATTAATTAGAAATGTAATTTTTATGGGACGGAGGGAG[T/A]
ACTACCTACTCCCGGTGGCTTTCCTTTCCTGGCAGCCTCCGATAAAGTGTCATAAATTGGAGGTCGGCAAACAATGTTTAAATTATAAAAAGCTGGACAC

Reverse complement sequence

GTGTCCAGCTTTTTATAATTTAAACATTGTTTGCCGACCTCCAATTTATGACACTTTATCGGAGGCTGCCAGGAAAGGAAAGCCACCGGGAGTAGGTAGT[A/T]
CTCCCTCCGTCCCATAAAAATTACATTTCTAATTAATTTAGGACCAAACAGTAGGATTAGAAAATGACCACAATGACCTTATTTAATGTACCCATTGCAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.60% 7.90% 1.57% 0.00% NA
All Indica  2759 84.00% 13.40% 2.61% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.20% 7.70% 5.04% 0.00% NA
Indica II  465 89.00% 8.00% 3.01% 0.00% NA
Indica III  913 75.50% 23.90% 0.66% 0.00% NA
Indica Intermediate  786 88.40% 8.80% 2.80% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 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
vg0225028520 T -> A LOC_Os02g41690.1 upstream_gene_variant ; 3697.0bp to feature; MODIFIER silent_mutation Average:69.044; most accessible tissue: Minghui63 root, score: 98.153 N N N N
vg0225028520 T -> A LOC_Os02g41680-LOC_Os02g41690 intergenic_region ; MODIFIER silent_mutation Average:69.044; most accessible tissue: Minghui63 root, score: 98.153 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)
vg0225028520 T A -0.19 -0.11 -0.06 -0.12 -0.11 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225028520 4.27E-07 NA mr1686 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
vg0225028520 1.73E-06 5.56E-08 mr1686 Ind_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
vg0225028520 NA 2.45E-06 mr1744 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
vg0225028520 NA 1.09E-07 mr1925 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
vg0225028520 NA 1.07E-06 mr1951 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
vg0225028520 NA 2.09E-09 mr1498_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
vg0225028520 NA 6.38E-07 mr1498_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
vg0225028520 NA 4.46E-09 mr1769_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
vg0225028520 NA 7.73E-07 mr1951_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
vg0225028520 NA 3.12E-07 mr1951_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