Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1223337361:

Variant ID: vg1223337361 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23337361
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGGCGTCGGAGGAGGAGAGGACAGATGGGAGGAAGAAGGCCAGCCGGTGGGCCGGCGAGATGTATATGGGTCCGAACGAAATGGGCCGCTAGTTTCGT[A/T]
GTAAATCCCATCCCGGCCCATGTCATATAGGCCACACGTTGGTAGCAGTTTCCGCGCGGAAAAAGTCTATATAGACTCCACAAGCATTAGCCGAATCCCA

Reverse complement sequence

TGGGATTCGGCTAATGCTTGTGGAGTCTATATAGACTTTTTCCGCGCGGAAACTGCTACCAACGTGTGGCCTATATGACATGGGCCGGGATGGGATTTAC[T/A]
ACGAAACTAGCGGCCCATTTCGTTCGGACCCATATACATCTCGCCGGCCCACCGGCTGGCCTTCTTCCTCCCATCTGTCCTCTCCTCCTCCGACGCCCCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 1.90% 0.44% 0.00% NA
All Indica  2759 96.00% 3.20% 0.76% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.60% 7.40% 2.02% 0.00% NA
Indica II  465 98.90% 0.90% 0.22% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 2.30% 1.02% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg1223337361 A -> T LOC_Os12g37980.1 downstream_gene_variant ; 539.0bp to feature; MODIFIER silent_mutation Average:95.363; most accessible tissue: Minghui63 root, score: 98.859 N N N N
vg1223337361 A -> T LOC_Os12g37970-LOC_Os12g37980 intergenic_region ; MODIFIER silent_mutation Average:95.363; most accessible tissue: Minghui63 root, score: 98.859 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)
vg1223337361 A T 0.01 0.03 0.03 0.0 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223337361 1.87E-06 3.71E-10 mr1038 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
vg1223337361 7.18E-06 1.84E-09 mr1038 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
vg1223337361 2.26E-06 NA mr1141 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
vg1223337361 6.24E-06 NA mr1141 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
vg1223337361 2.42E-07 3.09E-11 mr1389 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
vg1223337361 3.23E-06 2.07E-09 mr1389 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
vg1223337361 9.77E-07 1.12E-10 mr1038_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
vg1223337361 3.40E-06 3.18E-09 mr1038_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
vg1223337361 1.20E-08 1.04E-12 mr1389_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
vg1223337361 8.88E-08 1.96E-11 mr1389_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