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Detailed information for vg0824506465:

Variant ID: vg0824506465 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24506465
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


GTAACACAAAATAAGCCCCAAAAGGACGGCGCCATGTTGGGGGACGGCGCCATCCACTCTGGTGCCCCAAAAGGACTATTTCCGGTTTAAGTTTTTTCAG[G/A]
GGTCCATTTATAAAATATTTTTTTCAAAAAAGGACCAAAATGTAAAAATTTCAGGTAGAAGGCAGGGGGTGGGGGTTCGTGCGGGCGACGCAAGGTATGA

Reverse complement sequence

TCATACCTTGCGTCGCCCGCACGAACCCCCACCCCCTGCCTTCTACCTGAAATTTTTACATTTTGGTCCTTTTTTGAAAAAAATATTTTATAAATGGACC[C/T]
CTGAAAAAACTTAAACCGGAAATAGTCCTTTTGGGGCACCAGAGTGGATGGCGCCGTCCCCCAACATGGCGCCGTCCTTTTGGGGCTTATTTTGTGTTAC

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 87.70% 11.70% 0.21% 0.36% NA
All Indica  2759 80.30% 18.90% 0.18% 0.62% NA
All Japonica  1512 98.30% 1.50% 0.20% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 84.70% 14.80% 0.22% 0.22% NA
Indica III  913 62.10% 36.00% 0.44% 1.42% NA
Indica Intermediate  786 85.90% 13.70% 0.00% 0.38% NA
Temperate Japonica  767 99.10% 0.80% 0.13% 0.00% NA
Tropical Japonica  504 98.80% 1.00% 0.20% 0.00% NA
Japonica Intermediate  241 94.60% 5.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 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
vg0824506465 G -> A LOC_Os08g38760.1 intron_variant ; MODIFIER silent_mutation Average:74.251; most accessible tissue: Zhenshan97 panicle, score: 91.845 N N N N
vg0824506465 G -> DEL N N silent_mutation Average:74.251; most accessible tissue: Zhenshan97 panicle, score: 91.845 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)
vg0824506465 G A 0.02 0.01 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824506465 2.54E-06 NA mr1305 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
vg0824506465 1.09E-07 NA mr1586 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