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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0224509607:

Variant ID: vg0224509607 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24509607
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


AAACACCGTGTTTAGATCTAAATTTTTCTTAAAACTTCTAACTTTTTCATCACATCAAAACTTTCCTACACACATAAACTTTAAATTTTTTCGTTACATC[G/A,T]
TTCGAATTTCAACCAAACTTTCAATTTTAGCGTGAGCTAAACACAGCCAAATCACGGTGACAATGGACTAGCTCAGCAGGCAGGCAAAGCACAGGCAAAT

Reverse complement sequence

ATTTGCCTGTGCTTTGCCTGCCTGCTGAGCTAGTCCATTGTCACCGTGATTTGGCTGTGTTTAGCTCACGCTAAAATTGAAAGTTTGGTTGAAATTCGAA[C/T,A]
GATGTAACGAAAAAATTTAAAGTTTATGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTAGAAGTTTTAAGAAAAATTTAGATCTAAACACGGTGTTT

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 76.10% 22.60% 0.15% 1.02% T: 0.13%
All Indica  2759 80.80% 18.90% 0.11% 0.22% T: 0.04%
All Japonica  1512 66.10% 31.00% 0.20% 2.65% NA
Aus  269 83.30% 14.50% 0.37% 0.00% T: 1.86%
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 65.80% 34.00% 0.00% 0.22% NA
Indica III  913 78.00% 21.70% 0.22% 0.11% NA
Indica Intermediate  786 79.00% 20.20% 0.13% 0.51% T: 0.13%
Temperate Japonica  767 59.50% 36.10% 0.26% 4.17% NA
Tropical Japonica  504 80.00% 19.60% 0.00% 0.40% NA
Japonica Intermediate  241 58.50% 38.60% 0.41% 2.49% NA
VI/Aromatic  96 84.40% 13.50% 0.00% 2.08% NA
Intermediate  90 70.00% 30.00% 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
vg0224509607 G -> A LOC_Os02g40430-LOC_Os02g40440 intergenic_region ; MODIFIER silent_mutation Average:63.807; most accessible tissue: Zhenshan97 panicle, score: 88.625 N N N N
vg0224509607 G -> T LOC_Os02g40430-LOC_Os02g40440 intergenic_region ; MODIFIER silent_mutation Average:63.807; most accessible tissue: Zhenshan97 panicle, score: 88.625 N N N N
vg0224509607 G -> DEL N N silent_mutation Average:63.807; most accessible tissue: Zhenshan97 panicle, score: 88.625 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)
vg0224509607 G A 0.0 0.0 0.0 -0.01 0.0 0.0
vg0224509607 G T 0.01 0.01 0.01 -0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224509607 NA 7.20E-07 mr1071 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
vg0224509607 NA 9.41E-08 mr1080 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
vg0224509607 NA 2.06E-06 mr1124 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
vg0224509607 NA 9.93E-07 mr1150 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
vg0224509607 NA 1.10E-06 mr1613 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
vg0224509607 NA 4.82E-08 mr1619 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
vg0224509607 NA 2.02E-08 mr1795 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
vg0224509607 3.34E-06 3.34E-06 mr1908 Jap_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
vg0224509607 NA 6.76E-07 mr1918 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
vg0224509607 NA 1.80E-10 mr1962 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
vg0224509607 NA 2.47E-06 mr1074_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
vg0224509607 NA 2.15E-06 mr1098_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
vg0224509607 NA 4.47E-06 mr1099_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
vg0224509607 NA 5.63E-06 mr1148_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
vg0224509607 NA 4.20E-09 mr1150_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
vg0224509607 NA 3.06E-06 mr1795_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
vg0224509607 NA 2.67E-06 mr1871_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
vg0224509607 NA 2.78E-06 mr1918_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
vg0224509607 NA 1.11E-09 mr1962_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