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Detailed information for vg0332920303:

Variant ID: vg0332920303 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 32920303
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCATCCCACGCTTGCACCCCCGCGTGTATGAGCCGGGGCTTTTAACTATTTACCCATATGTCATAAACACATAAGGGTCCATGTGTCATTGACAGAGC[A/G]
TGGCAAATCGTTAATTGCAATGTCACAAGAGTGGCAAATAGTTAAATGTCCCGTATGAGCCGGGCCTAGCTGAGGAGCTACGGCCGATTCTTGCGTTTCC

Reverse complement sequence

GGAAACGCAAGAATCGGCCGTAGCTCCTCAGCTAGGCCCGGCTCATACGGGACATTTAACTATTTGCCACTCTTGTGACATTGCAATTAACGATTTGCCA[T/C]
GCTCTGTCAATGACACATGGACCCTTATGTGTTTATGACATATGGGTAAATAGTTAAAAGCCCCGGCTCATACACGCGGGGGTGCAAGCGTGGGATGAGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.00% 1.80% 1.21% 54.02% NA
All Indica  2759 13.00% 2.90% 1.09% 82.96% NA
All Japonica  1512 99.40% 0.00% 0.00% 0.60% NA
Aus  269 6.70% 0.00% 9.29% 84.01% NA
Indica I  595 4.20% 3.20% 1.68% 90.92% NA
Indica II  465 21.10% 4.70% 0.86% 73.33% NA
Indica III  913 12.20% 1.30% 0.00% 86.53% NA
Indica Intermediate  786 15.90% 3.60% 2.04% 78.50% NA
Temperate Japonica  767 99.50% 0.00% 0.00% 0.52% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 64.40% 2.20% 2.22% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0332920303 A -> DEL N N silent_mutation Average:95.032; most accessible tissue: Callus, score: 99.507 N N N N
vg0332920303 A -> G LOC_Os03g57770.1 downstream_gene_variant ; 68.0bp to feature; MODIFIER silent_mutation Average:95.032; most accessible tissue: Callus, score: 99.507 N N N N
vg0332920303 A -> G LOC_Os03g57770-LOC_Os03g57780 intergenic_region ; MODIFIER silent_mutation Average:95.032; most accessible tissue: Callus, score: 99.507 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)
vg0332920303 A G -0.16 -0.07 -0.07 -0.06 -0.11 -0.13

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0332920303 NA 1.09E-26 mr1037 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
vg0332920303 NA 1.25E-06 mr1796 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
vg0332920303 NA 1.74E-09 mr1860 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
vg0332920303 NA 9.22E-13 mr1940 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
vg0332920303 NA 5.28E-31 mr1037_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
vg0332920303 NA 1.70E-26 mr1051_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
vg0332920303 NA 3.17E-12 mr1189_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
vg0332920303 NA 5.85E-13 mr1514_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
vg0332920303 NA 2.32E-20 mr1531_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
vg0332920303 NA 2.12E-31 mr1598_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
vg0332920303 NA 3.53E-11 mr1728_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
vg0332920303 NA 7.40E-12 mr1734_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
vg0332920303 NA 2.24E-11 mr1782_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
vg0332920303 3.92E-07 2.14E-11 mr1860_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
vg0332920303 NA 4.88E-06 mr1860_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
vg0332920303 NA 1.95E-08 mr1940_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