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Detailed information for vg0518410596:

Variant ID: vg0518410596 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18410596
Reference Allele: AAlternative Allele: C,T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAGGTAATAGTTGTTGAATTTATCATAAAAATATATATATTGCTAAAAGTAAATAGTAAAGTGGAGCCATATATTACAATAGAAAAATGAGATAGATAT[A/C,T]
GGAGGAAAGATGAATGGCTGATGGAGTAATAGGGAATGAATGGAAGAGAGAAATTTTAATACTATTTGTTAAGTTCTTATGACCTGGTAATAGGTCTATT

Reverse complement sequence

AATAGACCTATTACCAGGTCATAAGAACTTAACAAATAGTATTAAAATTTCTCTCTTCCATTCATTCCCTATTACTCCATCAGCCATTCATCTTTCCTCC[T/G,A]
ATATCTATCTCATTTTTCTATTGTAATATATGGCTCCACTTTACTATTTACTTTTAGCAATATATATATTTTTATGATAAATTCAACAACTATTACCTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.90% 30.10% 17.29% 12.57% C: 0.17%
All Indica  2759 56.20% 7.70% 19.79% 16.02% C: 0.25%
All Japonica  1512 2.90% 72.40% 16.60% 8.13% NA
Aus  269 92.90% 0.40% 1.86% 4.83% NA
Indica I  595 79.80% 1.00% 12.44% 6.72% NA
Indica II  465 28.00% 21.30% 22.80% 27.74% C: 0.22%
Indica III  913 55.00% 3.80% 22.34% 18.40% C: 0.44%
Indica Intermediate  786 56.50% 9.30% 20.61% 13.36% C: 0.25%
Temperate Japonica  767 0.80% 79.30% 14.99% 4.95% NA
Tropical Japonica  504 6.90% 69.00% 13.69% 10.32% NA
Japonica Intermediate  241 1.20% 57.30% 27.80% 13.69% NA
VI/Aromatic  96 6.20% 84.40% 5.21% 4.17% NA
Intermediate  90 36.70% 37.80% 11.11% 13.33% C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0518410596 A -> T LOC_Os05g31620.1 upstream_gene_variant ; 3138.0bp to feature; MODIFIER silent_mutation Average:75.085; most accessible tissue: Minghui63 root, score: 89.131 N N N N
vg0518410596 A -> T LOC_Os05g31620-LOC_Os05g31630 intergenic_region ; MODIFIER silent_mutation Average:75.085; most accessible tissue: Minghui63 root, score: 89.131 N N N N
vg0518410596 A -> DEL N N silent_mutation Average:75.085; most accessible tissue: Minghui63 root, score: 89.131 N N N N
vg0518410596 A -> C LOC_Os05g31620.1 upstream_gene_variant ; 3138.0bp to feature; MODIFIER silent_mutation Average:75.085; most accessible tissue: Minghui63 root, score: 89.131 N N N N
vg0518410596 A -> C LOC_Os05g31620-LOC_Os05g31630 intergenic_region ; MODIFIER silent_mutation Average:75.085; most accessible tissue: Minghui63 root, score: 89.131 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)
vg0518410596 A C 0.0 0.0 0.0 -0.02 -0.01 0.0
vg0518410596 A T -0.01 -0.01 -0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518410596 NA 2.24E-06 mr1044 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
vg0518410596 NA 2.73E-13 mr1149 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
vg0518410596 NA 2.62E-07 mr1162 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
vg0518410596 NA 2.09E-10 mr1277 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
vg0518410596 NA 4.19E-09 mr1399 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
vg0518410596 NA 4.43E-13 mr1441 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
vg0518410596 NA 8.41E-06 mr1715 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
vg0518410596 NA 2.62E-13 mr1740 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
vg0518410596 NA 4.07E-07 mr1806 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
vg0518410596 NA 1.65E-08 mr1830 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
vg0518410596 NA 4.28E-13 mr1902 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
vg0518410596 NA 3.30E-25 mr1403_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
vg0518410596 NA 4.81E-06 mr1403_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
vg0518410596 NA 1.55E-26 mr1441_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
vg0518410596 NA 1.63E-10 mr1537_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
vg0518410596 NA 4.36E-13 mr1713_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
vg0518410596 NA 5.73E-06 mr1785_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
vg0518410596 NA 3.44E-08 mr1830_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
vg0518410596 NA 1.16E-07 mr1837_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
vg0518410596 NA 4.04E-19 mr1874_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