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Detailed information for vg1218012774:

Variant ID: vg1218012774 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18012774
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCGGAGAGAGGGAAGGAGGAGATAAAAAAAGAGAGGATTCTTGCCTGAGTAAAGAGGCCAGTCCTGCAGCTCCTCCTCCACCTGGCCGAGGCCGACCA[A/G]
CTGCTGCTACTGCTGCTGCTGCTGCTGAGGCGCCGATCGATCGAGGCCGGATCGAGGCAGCATACGATCGAGCGCCTATGGCCTATGGGGTCGGGGCTGA

Reverse complement sequence

TCAGCCCCGACCCCATAGGCCATAGGCGCTCGATCGTATGCTGCCTCGATCCGGCCTCGATCGATCGGCGCCTCAGCAGCAGCAGCAGCAGTAGCAGCAG[T/C]
TGGTCGGCCTCGGCCAGGTGGAGGAGGAGCTGCAGGACTGGCCTCTTTACTCAGGCAAGAATCCTCTCTTTTTTTATCTCCTCCTTCCCTCTCTCCGCAC

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 82.10% 0.60% 1.88% 15.36% NA
All Indica  2759 82.60% 1.10% 2.97% 13.30% NA
All Japonica  1512 88.30% 0.00% 0.13% 11.57% NA
Aus  269 40.90% 0.00% 1.49% 57.62% NA
Indica I  595 91.40% 0.20% 7.56% 0.84% NA
Indica II  465 65.20% 0.40% 2.37% 32.04% NA
Indica III  913 82.40% 2.40% 0.22% 15.01% NA
Indica Intermediate  786 86.60% 0.60% 3.05% 9.67% NA
Temperate Japonica  767 99.50% 0.00% 0.13% 0.39% NA
Tropical Japonica  504 77.60% 0.00% 0.00% 22.42% NA
Japonica Intermediate  241 75.10% 0.00% 0.41% 24.48% NA
VI/Aromatic  96 78.10% 0.00% 1.04% 20.83% NA
Intermediate  90 90.00% 0.00% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218012774 A -> DEL N N silent_mutation Average:52.114; most accessible tissue: Zhenshan97 root, score: 96.17 N N N N
vg1218012774 A -> G LOC_Os12g30070.1 upstream_gene_variant ; 2521.0bp to feature; MODIFIER silent_mutation Average:52.114; most accessible tissue: Zhenshan97 root, score: 96.17 N N N N
vg1218012774 A -> G LOC_Os12g30080.1 downstream_gene_variant ; 323.0bp to feature; MODIFIER silent_mutation Average:52.114; most accessible tissue: Zhenshan97 root, score: 96.17 N N N N
vg1218012774 A -> G LOC_Os12g30070-LOC_Os12g30080 intergenic_region ; MODIFIER silent_mutation Average:52.114; most accessible tissue: Zhenshan97 root, score: 96.17 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)
vg1218012774 A G 0.03 0.02 0.02 0.04 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218012774 NA 3.43E-08 mr1060 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
vg1218012774 NA 8.50E-06 mr1171 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
vg1218012774 NA 1.00E-05 mr1937 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