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Detailed information for vg0402919496:

Variant ID: vg0402919496 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2919496
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


GATCTTGATCCATGGTGGCTCTCATACCCGATCCCCAGGGTGTGGTCAGGGTAACTTCTCTACGTCTACAGTCGATTACTCCCCTATTCTTTGTTAACCA[A/T]
TCCATACCTAATATAACATCAAGGGTCTGTGGTACCAAGACCATAAGGTTAGAGGGAAATACCACATCCCTAAGGCGAATAGGTACATCAATGCAAGCTG

Reverse complement sequence

CAGCTTGCATTGATGTACCTATTCGCCTTAGGGATGTGGTATTTCCCTCTAACCTTATGGTCTTGGTACCACAGACCCTTGATGTTATATTAGGTATGGA[T/A]
TGGTTAACAAAGAATAGGGGAGTAATCGACTGTAGACGTAGAGAAGTTACCCTGACCACACCCTGGGGATCGGGTATGAGAGCCACCATGGATCAAGATC

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 59.50% 15.10% 5.69% 19.76% NA
All Indica  2759 39.10% 25.50% 8.81% 26.64% NA
All Japonica  1512 95.70% 0.10% 0.33% 3.84% NA
Aus  269 63.20% 0.40% 6.32% 30.11% NA
Indica I  595 20.00% 3.70% 3.19% 73.11% NA
Indica II  465 51.40% 26.50% 13.33% 8.82% NA
Indica III  913 37.90% 40.40% 6.90% 14.79% NA
Indica Intermediate  786 47.60% 24.00% 12.60% 15.78% NA
Temperate Japonica  767 95.00% 0.00% 0.13% 4.82% NA
Tropical Japonica  504 95.60% 0.20% 0.40% 3.77% NA
Japonica Intermediate  241 97.90% 0.40% 0.83% 0.83% NA
VI/Aromatic  96 54.20% 1.00% 1.04% 43.75% NA
Intermediate  90 71.10% 5.60% 3.33% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402919496 A -> DEL LOC_Os04g05710.1 N frameshift_variant Average:38.756; most accessible tissue: Minghui63 flag leaf, score: 88.907 N N N N
vg0402919496 A -> T LOC_Os04g05710.1 missense_variant ; p.Asp545Glu; MODERATE nonsynonymous_codon ; D545E Average:38.756; most accessible tissue: Minghui63 flag leaf, score: 88.907 benign 1.241 DELETERIOUS 0.00

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)
vg0402919496 A T -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402919496 NA 7.06E-10 mr1498 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
vg0402919496 NA 1.93E-09 mr1498 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
vg0402919496 NA 1.15E-06 mr1925 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
vg0402919496 2.69E-08 3.16E-13 mr1951 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
vg0402919496 8.26E-08 4.58E-11 mr1951 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