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Detailed information for vg0413769010:

Variant ID: vg0413769010 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13769010
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


TTTAAGTCTAATTGCACCATGATTTAGCAATATGGTGCTGCAGTAAACATTTGCTAACGACGATTAATTAGGCTTAATATATTCATCTCGCGATTTATAG[A/G]
CGGATTTTGTAATTTATTTTTTTATTAGACTATATTTAATACTCCAAATGTGTATCCATATATCCGATGTGACATACCAAAATATTACACCCTGAATCTA

Reverse complement sequence

TAGATTCAGGGTGTAATATTTTGGTATGTCACATCGGATATATGGATACACATTTGGAGTATTAAATATAGTCTAATAAAAAAATAAATTACAAAATCCG[T/C]
CTATAAATCGCGAGATGAATATATTAAGCCTAATTAATCGTCGTTAGCAAATGTTTACTGCAGCACCATATTGCTAAATCATGGTGCAATTAGACTTAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.80% 45.00% 0.15% 0.00% NA
All Indica  2759 74.40% 25.30% 0.25% 0.00% NA
All Japonica  1512 9.60% 90.40% 0.00% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 46.40% 52.80% 0.84% 0.00% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 85.80% 14.20% 0.00% 0.00% NA
Indica Intermediate  786 71.10% 28.80% 0.13% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 14.50% 85.50% 0.00% 0.00% NA
Japonica Intermediate  241 23.70% 76.30% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 58.90% 41.10% 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
vg0413769010 A -> G LOC_Os04g24100.1 upstream_gene_variant ; 2475.0bp to feature; MODIFIER silent_mutation Average:65.763; most accessible tissue: Zhenshan97 flower, score: 87.365 N N N N
vg0413769010 A -> G LOC_Os04g24110.1 upstream_gene_variant ; 2311.0bp to feature; MODIFIER silent_mutation Average:65.763; most accessible tissue: Zhenshan97 flower, score: 87.365 N N N N
vg0413769010 A -> G LOC_Os04g24100-LOC_Os04g24110 intergenic_region ; MODIFIER silent_mutation Average:65.763; most accessible tissue: Zhenshan97 flower, score: 87.365 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)
vg0413769010 A G -0.05 -0.08 -0.05 0.0 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413769010 4.73E-08 1.65E-10 mr1350_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
vg0413769010 3.04E-06 NA mr1584_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
vg0413769010 3.92E-07 1.14E-07 mr1730_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