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Detailed information for vg0306923245:

Variant ID: vg0306923245 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 6923245
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTTTTCCCTCGTGAGCGAGACACCGGGGGCCACGGTGCATTTAGCCACAGCCCCATTTGCCTCCATTAGAGCAAGTTTAATAGTATAGCCAACTACTA[G/A]
CTCCAAATTATCTATAACCAATTCATATAATAGTTGCTTGCTATACTATTAATATCTGATCCCACCTGTCATACACACATTACGTCTTGGAGTCCGTGCT

Reverse complement sequence

AGCACGGACTCCAAGACGTAATGTGTGTATGACAGGTGGGATCAGATATTAATAGTATAGCAAGCAACTATTATATGAATTGGTTATAGATAATTTGGAG[C/T]
TAGTAGTTGGCTATACTATTAAACTTGCTCTAATGGAGGCAAATGGGGCTGTGGCTAAATGCACCGTGGCCCCCGGTGTCTCGCTCACGAGGGAAAAACA

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 65.30% 34.60% 0.13% 0.04% NA
All Indica  2759 52.40% 47.30% 0.18% 0.07% NA
All Japonica  1512 97.30% 2.70% 0.00% 0.00% NA
Aus  269 12.30% 87.70% 0.00% 0.00% NA
Indica I  595 69.60% 30.10% 0.17% 0.17% NA
Indica II  465 69.90% 30.10% 0.00% 0.00% NA
Indica III  913 34.60% 65.20% 0.11% 0.11% NA
Indica Intermediate  786 49.90% 49.70% 0.38% 0.00% NA
Temperate Japonica  767 97.00% 3.00% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 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
vg0306923245 G -> A LOC_Os03g12850-LOC_Os03g12860 intergenic_region ; MODIFIER silent_mutation Average:90.746; most accessible tissue: Callus, score: 98.102 N N N N
vg0306923245 G -> DEL N N silent_mutation Average:90.746; most accessible tissue: Callus, score: 98.102 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)
vg0306923245 G A -0.03 -0.08 -0.03 -0.01 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306923245 NA 8.68E-07 mr1587 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
vg0306923245 NA 8.11E-06 mr1654 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
vg0306923245 NA 8.07E-06 mr1821 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
vg0306923245 NA 3.32E-11 mr1193_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
vg0306923245 NA 1.44E-11 mr1654_2 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
vg0306923245 NA 2.11E-07 mr1654_2 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