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Detailed information for vg0217411971:

Variant ID: vg0217411971 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17411971
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGTCGAGAAAAAAAAATTTACGTGCAAATATGATTTGACAGGAGGGAGAGAAAGTAGACTTATTCCAGGAGAGGCTCATAAAAAGGTAGACTTATTCC[G/A]
AGAGGCCCATAGAAACGGTGCAAGTAATATAGGTGTAAAAAGGAGAGAGAGGTGATTACATGGAAGATACATATACTATATCAACCACGGTTTTGACCCG

Reverse complement sequence

CGGGTCAAAACCGTGGTTGATATAGTATATGTATCTTCCATGTAATCACCTCTCTCTCCTTTTTACACCTATATTACTTGCACCGTTTCTATGGGCCTCT[C/T]
GGAATAAGTCTACCTTTTTATGAGCCTCTCCTGGAATAAGTCTACTTTCTCTCCCTCCTGTCAAATCATATTTGCACGTAAATTTTTTTTTCTCGACCAC

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 67.80% 19.00% 2.39% 10.75% NA
All Indica  2759 47.90% 30.40% 3.99% 17.69% NA
All Japonica  1512 99.10% 0.30% 0.07% 0.60% NA
Aus  269 84.00% 16.00% 0.00% 0.00% NA
Indica I  595 32.40% 33.80% 6.89% 26.89% NA
Indica II  465 52.70% 11.20% 6.67% 29.46% NA
Indica III  913 61.00% 38.70% 0.11% 0.22% NA
Indica Intermediate  786 41.50% 29.80% 4.71% 24.05% NA
Temperate Japonica  767 99.00% 0.10% 0.13% 0.78% NA
Tropical Japonica  504 99.40% 0.40% 0.00% 0.20% NA
Japonica Intermediate  241 98.80% 0.40% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 71.10% 14.40% 2.22% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0217411971 G -> A LOC_Os02g29300.1 upstream_gene_variant ; 791.0bp to feature; MODIFIER silent_mutation Average:92.953; most accessible tissue: Minghui63 panicle, score: 98.225 N N N N
vg0217411971 G -> A LOC_Os02g29320.1 upstream_gene_variant ; 4412.0bp to feature; MODIFIER silent_mutation Average:92.953; most accessible tissue: Minghui63 panicle, score: 98.225 N N N N
vg0217411971 G -> A LOC_Os02g29310.1 downstream_gene_variant ; 3333.0bp to feature; MODIFIER silent_mutation Average:92.953; most accessible tissue: Minghui63 panicle, score: 98.225 N N N N
vg0217411971 G -> A LOC_Os02g29300-LOC_Os02g29310 intergenic_region ; MODIFIER silent_mutation Average:92.953; most accessible tissue: Minghui63 panicle, score: 98.225 N N N N
vg0217411971 G -> DEL N N silent_mutation Average:92.953; most accessible tissue: Minghui63 panicle, score: 98.225 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)
vg0217411971 G A 0.02 0.03 0.04 0.01 0.03 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217411971 7.24E-07 7.54E-12 mr1317 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
vg0217411971 1.00E-06 1.00E-09 mr1317 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
vg0217411971 4.69E-06 1.44E-06 mr1585 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
vg0217411971 1.28E-06 7.24E-08 mr1603 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
vg0217411971 NA 6.69E-08 mr1610 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
vg0217411971 1.96E-06 2.82E-06 mr1818 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
vg0217411971 2.35E-07 NA mr1855 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
vg0217411971 1.47E-06 8.30E-12 mr1855 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
vg0217411971 4.86E-06 8.10E-14 mr1914 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
vg0217411971 4.02E-06 2.23E-07 mr1914 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
vg0217411971 3.28E-07 2.00E-12 mr1927 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
vg0217411971 3.18E-08 2.11E-10 mr1927 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
vg0217411971 1.40E-06 2.54E-10 mr1317_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
vg0217411971 1.39E-07 2.81E-11 mr1317_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
vg0217411971 NA 4.61E-06 mr1379_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
vg0217411971 NA 1.69E-06 mr1559_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
vg0217411971 6.69E-06 NA mr1610_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
vg0217411971 2.43E-06 1.94E-09 mr1610_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
vg0217411971 2.31E-06 NA mr1818_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
vg0217411971 7.30E-07 7.19E-09 mr1818_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
vg0217411971 3.55E-09 NA mr1855_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
vg0217411971 2.14E-08 2.08E-12 mr1855_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
vg0217411971 4.82E-07 NA mr1897_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
vg0217411971 3.99E-07 5.99E-10 mr1897_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
vg0217411971 2.07E-07 1.38E-13 mr1914_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
vg0217411971 2.90E-07 1.43E-12 mr1914_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
vg0217411971 5.95E-08 NA mr1927_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
vg0217411971 1.78E-07 2.82E-13 mr1927_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