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Detailed information for vg0227537488:

Variant ID: vg0227537488 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 27537488
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAATTGAGATCCCCTGTAGTACTGCATGTGTAGTACTGCAGACAACCTGCATCCATATTCTTCAATCTTTCTCTCTCCACCACAAGTTCAAGGACGTA[T/C]
CTAGGGAGGAGACACATGTCTAGGGTGGCATTGGATTTTGAGTTTGTTTATTCAAAATGTGAAAGTTTTGACTTTTCTAATAGACATTTTTTTGCCTCTT

Reverse complement sequence

AAGAGGCAAAAAAATGTCTATTAGAAAAGTCAAAACTTTCACATTTTGAATAAACAAACTCAAAATCCAATGCCACCCTAGACATGTGTCTCCTCCCTAG[A/G]
TACGTCCTTGAACTTGTGGTGGAGAGAGAAAGATTGAAGAATATGGATGCAGGTTGTCTGCAGTACTACACATGCAGTACTACAGGGGATCTCAATTGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.20% 10.00% 0.78% 0.00% NA
All Indica  2759 98.90% 1.00% 0.11% 0.00% NA
All Japonica  1512 69.40% 28.40% 2.25% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 98.30% 1.30% 0.34% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.00% 0.13% 0.00% NA
Temperate Japonica  767 46.50% 50.20% 3.26% 0.00% NA
Tropical Japonica  504 97.00% 2.40% 0.60% 0.00% NA
Japonica Intermediate  241 84.20% 13.30% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0227537488 T -> C LOC_Os02g45310.1 upstream_gene_variant ; 2865.0bp to feature; MODIFIER silent_mutation Average:85.542; most accessible tissue: Callus, score: 92.383 N N N N
vg0227537488 T -> C LOC_Os02g45310-LOC_Os02g45320 intergenic_region ; MODIFIER silent_mutation Average:85.542; most accessible tissue: Callus, score: 92.383 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)
vg0227537488 T C 0.02 0.01 0.02 0.03 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0227537488 NA 4.73E-07 mr1002 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
vg0227537488 NA 1.69E-07 mr1977 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
vg0227537488 NA 6.01E-10 mr1010_2 Jap_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
vg0227537488 NA 1.79E-10 mr1530_2 Jap_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
vg0227537488 NA 2.11E-07 mr1627_2 Jap_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
vg0227537488 NA 5.22E-07 mr1952_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
vg0227537488 5.17E-07 5.73E-10 mr1977_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
vg0227537488 2.22E-07 2.45E-08 mr1977_2 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