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Detailed information for vg0503455480:

Variant ID: vg0503455480 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3455480
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CTGTCTCAGAGATTTTCAGCCAGACTTTCTAATCAAAGGAGGATGCATGGCACAAGGCCATATCAGGACTCACCAGGAGTAGCCCCACATTCATACTTGG[G/A]
TGTCTGGTTTTGCCTTTTTGTTCCTAAATATTTTCAGAATTTTAGGCCATACCTTTTCTCCATGTTGTACTAATGTCTTCCTTAATTAGGTTAATTATTG

Reverse complement sequence

CAATAATTAACCTAATTAAGGAAGACATTAGTACAACATGGAGAAAAGGTATGGCCTAAAATTCTGAAAATATTTAGGAACAAAAAGGCAAAACCAGACA[C/T]
CCAAGTATGAATGTGGGGCTACTCCTGGTGAGTCCTGATATGGCCTTGTGCCATGCATCCTCCTTTGATTAGAAAGTCTGGCTGAAAATCTCTGAGACAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.30% 13.60% 0.08% 0.00% NA
All Indica  2759 77.30% 22.50% 0.14% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 89.60% 10.30% 0.17% 0.00% NA
Indica II  465 62.60% 37.20% 0.22% 0.00% NA
Indica III  913 77.20% 22.70% 0.11% 0.00% NA
Indica Intermediate  786 77.00% 22.90% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0503455480 G -> A LOC_Os05g06670.1 upstream_gene_variant ; 4136.0bp to feature; MODIFIER silent_mutation Average:57.268; most accessible tissue: Zhenshan97 flower, score: 99.022 N N N N
vg0503455480 G -> A LOC_Os05g06660-LOC_Os05g06670 intergenic_region ; MODIFIER silent_mutation Average:57.268; most accessible tissue: Zhenshan97 flower, score: 99.022 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)
vg0503455480 G A -0.05 0.02 -0.01 -0.01 -0.11 -0.22

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503455480 NA 9.20E-06 mr1044 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
vg0503455480 1.80E-06 NA mr1577 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
vg0503455480 2.39E-06 NA mr1577 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
vg0503455480 4.44E-08 9.81E-09 mr1792 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
vg0503455480 2.43E-07 2.80E-07 mr1792 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
vg0503455480 NA 7.27E-10 mr1794 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
vg0503455480 NA 1.09E-06 mr1425_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
vg0503455480 NA 8.84E-06 mr1456_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