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Detailed information for vg1207383759:

Variant ID: vg1207383759 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7383759
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTGAGCTACGCATATATATACGGAAGGATTAGTGGTGAATTAGTCATCAAGTTTCATCCGATCCACGAACGAACTAGAACAGTGGGCTAGCTATAGCG[A/G]
GTATTAGGGCTTACTGTTGTCCTGGTCCGCAGCATTGTTGATGTAGAGACGAATCCATCCCAAATCTTGGCGAACTGCTGGGAGGATTTGCAGGAGGAGG

Reverse complement sequence

CCTCCTCCTGCAAATCCTCCCAGCAGTTCGCCAAGATTTGGGATGGATTCGTCTCTACATCAACAATGCTGCGGACCAGGACAACAGTAAGCCCTAATAC[T/C]
CGCTATAGCTAGCCCACTGTTCTAGTTCGTTCGTGGATCGGATGAAACTTGATGACTAATTCACCACTAATCCTTCCGTATATATATGCGTAGCTCAACT

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 91.20% 0.70% 0.08% 7.96% NA
All Indica  2759 87.40% 0.20% 0.11% 12.29% NA
All Japonica  1512 97.70% 0.10% 0.07% 2.18% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.00% 0.34% NA
Indica II  465 56.30% 0.20% 0.22% 43.23% NA
Indica III  913 96.30% 0.30% 0.00% 3.40% NA
Indica Intermediate  786 86.30% 0.10% 0.25% 13.36% NA
Temperate Japonica  767 96.00% 0.00% 0.13% 3.91% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 89.60% 9.40% 0.00% 1.04% NA
Intermediate  90 95.60% 1.10% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1207383759 A -> DEL N N silent_mutation Average:86.687; most accessible tissue: Minghui63 flag leaf, score: 90.43 N N N N
vg1207383759 A -> G LOC_Os12g13280.1 downstream_gene_variant ; 1947.0bp to feature; MODIFIER silent_mutation Average:86.687; most accessible tissue: Minghui63 flag leaf, score: 90.43 N N N N
vg1207383759 A -> G LOC_Os12g13270.1 intron_variant ; MODIFIER silent_mutation Average:86.687; most accessible tissue: Minghui63 flag leaf, score: 90.43 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)
vg1207383759 A G -0.01 -0.01 0.0 -0.01 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207383759 NA 1.63E-06 mr1272 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
vg1207383759 NA 8.31E-06 mr1864 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
vg1207383759 NA 6.76E-06 mr1952 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
vg1207383759 NA 6.02E-07 mr1227_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
vg1207383759 6.68E-07 6.68E-07 mr1853_2 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