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Detailed information for vg0313160369:

Variant ID: vg0313160369 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13160369
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTCACAATTATATTAATGCTAATGAATCTATTTATATTGATGTTAATGAATCTATATATTTAGATTCATTAACATCAATACAAATATAGAAAATGCTA[A/G]
AATAATTTACATTGTGAAACGGGGGAGGTAGAATTCATCCGGCCCATGGCCTCCGTAATCCTGATCTTGAAGCTACCGGTTTATCCAAAAGGAGAATCCT

Reverse complement sequence

AGGATTCTCCTTTTGGATAAACCGGTAGCTTCAAGATCAGGATTACGGAGGCCATGGGCCGGATGAATTCTACCTCCCCCGTTTCACAATGTAAATTATT[T/C]
TAGCATTTTCTATATTTGTATTGATGTTAATGAATCTAAATATATAGATTCATTAACATCAATATAAATAGATTCATTAGCATTAATATAATTGTGAGAA

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 89.30% 10.60% 0.08% 0.00% NA
All Indica  2759 85.40% 14.60% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 66.20% 33.10% 0.74% 0.00% NA
Indica I  595 90.80% 9.10% 0.17% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 74.30% 25.70% 0.00% 0.00% NA
Indica Intermediate  786 86.30% 13.60% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0313160369 A -> G LOC_Os03g22780.1 upstream_gene_variant ; 2965.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22790.1 upstream_gene_variant ; 1544.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22770.1 downstream_gene_variant ; 4825.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22800.1 downstream_gene_variant ; 4198.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22770.2 downstream_gene_variant ; 4825.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22800.3 downstream_gene_variant ; 4125.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22800.2 downstream_gene_variant ; 4198.0bp to feature; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 N N N N
vg0313160369 A -> G LOC_Os03g22780-LOC_Os03g22790 intergenic_region ; MODIFIER silent_mutation Average:91.798; most accessible tissue: Zhenshan97 flag leaf, score: 97.726 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)
vg0313160369 A G 0.0 -0.01 -0.02 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313160369 NA 6.62E-06 mr1397 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
vg0313160369 NA 8.16E-06 mr1400 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
vg0313160369 NA 1.96E-10 mr1730 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
vg0313160369 NA 3.69E-07 mr1762 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
vg0313160369 8.15E-06 NA mr1798 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
vg0313160369 3.24E-07 2.65E-11 mr1798 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
vg0313160369 NA 1.26E-08 mr1798_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