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Detailed information for vg0421318693:

Variant ID: vg0421318693 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21318693
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


GGAAAAATATCTCCTCATTTGCCAATAATAAGTGGAGGCAAGTAGGTCGTCTATTTCATTTCACCCATATTTAGGGCCCCCTTTGAATGCAAAAATAGTG[G/A]
AATATGAAAAATGCAAGATTTTAATAGGAATATAAGTACAAAACAGAGGATTGCAAAATACAGAAAAAGCAAAGGAAGGAATAGGATGAGAGAGATAGAT

Reverse complement sequence

ATCTATCTCTCTCATCCTATTCCTTCCTTTGCTTTTTCTGTATTTTGCAATCCTCTGTTTTGTACTTATATTCCTATTAAAATCTTGCATTTTTCATATT[C/T]
CACTATTTTTGCATTCAAAGGGGGCCCTAAATATGGGTGAAATGAAATAGACGACCTACTTGCCTCCACTTATTATTGGCAAATGAGGAGATATTTTTCC

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 85.10% 14.80% 0.06% 0.00% NA
All Indica  2759 75.00% 24.90% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 80.00% 19.80% 0.17% 0.00% NA
Indica II  465 81.70% 18.10% 0.22% 0.00% NA
Indica III  913 65.90% 34.00% 0.11% 0.00% NA
Indica Intermediate  786 77.60% 22.40% 0.00% 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 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0421318693 G -> A LOC_Os04g35070.1 upstream_gene_variant ; 924.0bp to feature; MODIFIER silent_mutation Average:74.897; most accessible tissue: Callus, score: 86.087 N N N N
vg0421318693 G -> A LOC_Os04g35080.1 upstream_gene_variant ; 4353.0bp to feature; MODIFIER silent_mutation Average:74.897; most accessible tissue: Callus, score: 86.087 N N N N
vg0421318693 G -> A LOC_Os04g35060.1 downstream_gene_variant ; 446.0bp to feature; MODIFIER silent_mutation Average:74.897; most accessible tissue: Callus, score: 86.087 N N N N
vg0421318693 G -> A LOC_Os04g35060-LOC_Os04g35070 intergenic_region ; MODIFIER silent_mutation Average:74.897; most accessible tissue: Callus, score: 86.087 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)
vg0421318693 G A -0.05 -0.02 -0.02 -0.02 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421318693 2.50E-06 NA mr1245_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
vg0421318693 9.13E-06 3.99E-06 mr1245_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
vg0421318693 3.25E-06 3.25E-06 mr1267_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
vg0421318693 6.61E-06 6.61E-06 mr1311_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
vg0421318693 1.71E-06 NA mr1373_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
vg0421318693 4.10E-06 1.25E-06 mr1373_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
vg0421318693 NA 2.77E-06 mr1655_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
vg0421318693 NA 9.91E-06 mr1669_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
vg0421318693 3.23E-06 3.23E-06 mr1688_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
vg0421318693 4.76E-06 4.76E-06 mr1983_2 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