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Detailed information for vg1206953771:

Variant ID: vg1206953771 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6953771
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


AACTGGATATTTCGACCCCTTCAACTATCAAAACCGGTGCAAACAATGCACCTGGGTGGTTTTGGATGACGTGACGGGCTTGACCGAATCTTTGTCCTAC[A/G]
TGGCGCTTACGTGACATTAGAATAAAAACAAAAAATAAAAGGAAATATGTGGGATCCATATTTCATTCACACAAATAAAGTATTGTGGGACCTACTGACA

Reverse complement sequence

TGTCAGTAGGTCCCACAATACTTTATTTGTGTGAATGAAATATGGATCCCACATATTTCCTTTTATTTTTTGTTTTTATTCTAATGTCACGTAAGCGCCA[T/C]
GTAGGACAAAGATTCGGTCAAGCCCGTCACGTCATCCAAAACCACCCAGGTGCATTGTTTGCACCGGTTTTGATAGTTGAAGGGGTCGAAATATCCAGTT

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 59.80% 40.00% 0.21% 0.00% NA
All Indica  2759 46.90% 52.90% 0.14% 0.00% NA
All Japonica  1512 74.20% 25.70% 0.13% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 84.70% 15.10% 0.17% 0.00% NA
Indica II  465 23.90% 75.90% 0.22% 0.00% NA
Indica III  913 28.50% 71.40% 0.11% 0.00% NA
Indica Intermediate  786 53.40% 46.40% 0.13% 0.00% NA
Temperate Japonica  767 73.10% 26.70% 0.13% 0.00% NA
Tropical Japonica  504 83.10% 16.90% 0.00% 0.00% NA
Japonica Intermediate  241 58.90% 40.70% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 66.70% 28.90% 4.44% 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
vg1206953771 A -> G LOC_Os12g12610.1 downstream_gene_variant ; 2262.0bp to feature; MODIFIER silent_mutation Average:93.466; most accessible tissue: Minghui63 panicle, score: 96.942 N N N N
vg1206953771 A -> G LOC_Os12g12620.1 downstream_gene_variant ; 2513.0bp to feature; MODIFIER silent_mutation Average:93.466; most accessible tissue: Minghui63 panicle, score: 96.942 N N N N
vg1206953771 A -> G LOC_Os12g12630.1 downstream_gene_variant ; 3966.0bp to feature; MODIFIER silent_mutation Average:93.466; most accessible tissue: Minghui63 panicle, score: 96.942 N N N N
vg1206953771 A -> G LOC_Os12g12610-LOC_Os12g12620 intergenic_region ; MODIFIER silent_mutation Average:93.466; most accessible tissue: Minghui63 panicle, score: 96.942 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)
vg1206953771 A G 0.02 0.01 0.01 0.02 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206953771 NA 5.11E-06 mr1057 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
vg1206953771 NA 4.06E-07 mr1500 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
vg1206953771 NA 2.63E-06 mr1531 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
vg1206953771 3.90E-07 3.89E-07 mr1673 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
vg1206953771 NA 7.60E-13 mr1565_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