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Detailed information for vg1105347465:

Variant ID: vg1105347465 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5347465
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAGATAACATGAAGAGTTGAGGAATGTACAATGAACTTATCCCTATATTTTGGTACAGAAGTAGTAGTATGCTAGTATTTGACAAGAACTGATCTTTT[A/T]
AGATCGCATAACAGCTTTATCAGCTATTATTTGATAAGGCTCTAAAAGAAAAGCTATGTTTCGACAAGAATGAAGTAAAAATGTCAATTTAAAACAACAC

Reverse complement sequence

GTGTTGTTTTAAATTGACATTTTTACTTCATTCTTGTCGAAACATAGCTTTTCTTTTAGAGCCTTATCAAATAATAGCTGATAAAGCTGTTATGCGATCT[T/A]
AAAAGATCAGTTCTTGTCAAATACTAGCATACTACTACTTCTGTACCAAAATATAGGGATAAGTTCATTGTACATTCCTCAACTCTTCATGTTATCTAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.90% 23.10% 0.02% 0.00% NA
All Indica  2759 92.00% 8.00% 0.00% 0.00% NA
All Japonica  1512 43.30% 56.60% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.00% 3.00% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 93.10% 6.90% 0.00% 0.00% NA
Indica Intermediate  786 84.00% 16.00% 0.00% 0.00% NA
Temperate Japonica  767 40.50% 59.30% 0.13% 0.00% NA
Tropical Japonica  504 39.30% 60.70% 0.00% 0.00% NA
Japonica Intermediate  241 60.60% 39.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1105347465 A -> T LOC_Os11g09970.1 upstream_gene_variant ; 1851.0bp to feature; MODIFIER silent_mutation Average:75.349; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg1105347465 A -> T LOC_Os11g09979.1 upstream_gene_variant ; 1721.0bp to feature; MODIFIER silent_mutation Average:75.349; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg1105347465 A -> T LOC_Os11g09979.2 upstream_gene_variant ; 1721.0bp to feature; MODIFIER silent_mutation Average:75.349; most accessible tissue: Zhenshan97 flower, score: 89.409 N N N N
vg1105347465 A -> T LOC_Os11g09970-LOC_Os11g09979 intergenic_region ; MODIFIER silent_mutation Average:75.349; most accessible tissue: Zhenshan97 flower, score: 89.409 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)
vg1105347465 A T 0.0 0.0 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105347465 5.64E-06 NA mr1182 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
vg1105347465 2.63E-06 NA mr1282 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
vg1105347465 4.59E-06 NA mr1650 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
vg1105347465 4.73E-07 4.31E-10 mr1658 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
vg1105347465 2.09E-06 NA mr1301_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