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Detailed information for vg0431806376:

Variant ID: vg0431806376 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31806376
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.13, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACCGGTAGTGCTTACTACTGCAGTAGTGAAGTGCTCCTACTGAATTCTACTACCATCCCAAAATATAACAATTTAGAATTAGATGAAACATATCCTA[A/G]
TCTAATAAATCTGGAGAACAAATTATTATATTTTGGGACCGAGGGAGTACCATTCTCTTAAACTACTTAATGAGTTGAGAATCTAGTGATGATGAAATTA

Reverse complement sequence

TAATTTCATCATCACTAGATTCTCAACTCATTAAGTAGTTTAAGAGAATGGTACTCCCTCGGTCCCAAAATATAATAATTTGTTCTCCAGATTTATTAGA[T/C]
TAGGATATGTTTCATCTAATTCTAAATTGTTATATTTTGGGATGGTAGTAGAATTCAGTAGGAGCACTTCACTACTGCAGTAGTAAGCACTACCGGTAAA

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 57.20% 42.10% 0.28% 0.44% NA
All Indica  2759 31.60% 67.30% 0.36% 0.76% NA
All Japonica  1512 96.10% 3.80% 0.13% 0.00% NA
Aus  269 85.10% 14.90% 0.00% 0.00% NA
Indica I  595 22.40% 77.10% 0.50% 0.00% NA
Indica II  465 53.30% 45.60% 0.00% 1.08% NA
Indica III  913 23.00% 75.40% 0.22% 1.42% NA
Indica Intermediate  786 35.60% 63.40% 0.64% 0.38% NA
Temperate Japonica  767 96.60% 3.10% 0.26% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 63.30% 35.60% 1.11% 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
vg0431806376 A -> DEL N N silent_mutation Average:68.249; most accessible tissue: Minghui63 root, score: 93.25 N N N N
vg0431806376 A -> G LOC_Os04g53400.1 upstream_gene_variant ; 3332.0bp to feature; MODIFIER silent_mutation Average:68.249; most accessible tissue: Minghui63 root, score: 93.25 N N N N
vg0431806376 A -> G LOC_Os04g53390.1 downstream_gene_variant ; 3144.0bp to feature; MODIFIER silent_mutation Average:68.249; most accessible tissue: Minghui63 root, score: 93.25 N N N N
vg0431806376 A -> G LOC_Os04g53390-LOC_Os04g53400 intergenic_region ; MODIFIER silent_mutation Average:68.249; most accessible tissue: Minghui63 root, score: 93.25 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)
vg0431806376 A G -0.05 -0.02 -0.01 -0.02 -0.03 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431806376 7.07E-07 2.15E-06 mr1642 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
vg0431806376 NA 2.92E-06 mr1968 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