Search for Variation information by Variation ID:

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

Detailed information for vg0112495464:

Variant ID: vg0112495464 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12495464
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.13, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAAGGGTGTGTTTGGATAATGGGAAATGAGGGGTGGGATTGGGATTGGGAAATGAATGAATAGTTAGGATTAAATGGAAGGGGGAGAATGAATGATTA[G/A]
AATTTAAATATGTCTTTTGATGGGTGGGAAATCATTTCCCTATCCCATTTGCCAAACATGGCCTAAGGGATATCAAATGAACTTATTCTAAAGGAAAATA

Reverse complement sequence

TATTTTCCTTTAGAATAAGTTCATTTGATATCCCTTAGGCCATGTTTGGCAAATGGGATAGGGAAATGATTTCCCACCCATCAAAAGACATATTTAAATT[C/T]
TAATCATTCATTCTCCCCCTTCCATTTAATCCTAACTATTCATTCATTTCCCAATCCCAATCCCACCCCTCATTTCCCATTATCCAAACACACCCTTAAC

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 51.30% 30.50% 0.95% 17.27% NA
All Indica  2759 80.50% 4.50% 0.80% 14.21% NA
All Japonica  1512 2.60% 80.10% 0.46% 16.87% NA
Aus  269 37.50% 0.70% 3.35% 58.36% NA
Indica I  595 95.00% 4.40% 0.17% 0.50% NA
Indica II  465 50.50% 5.40% 2.15% 41.94% NA
Indica III  913 90.00% 4.40% 0.44% 5.15% NA
Indica Intermediate  786 76.10% 4.30% 0.89% 18.70% NA
Temperate Japonica  767 0.80% 80.70% 0.52% 17.99% NA
Tropical Japonica  504 5.80% 87.70% 0.00% 6.55% NA
Japonica Intermediate  241 1.70% 62.20% 1.24% 34.85% NA
VI/Aromatic  96 30.20% 68.80% 0.00% 1.04% NA
Intermediate  90 38.90% 41.10% 7.78% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0112495464 G -> A LOC_Os01g22220.1 upstream_gene_variant ; 808.0bp to feature; MODIFIER silent_mutation Average:53.09; most accessible tissue: Callus, score: 93.836 N N N N
vg0112495464 G -> A LOC_Os01g22230.1 upstream_gene_variant ; 4459.0bp to feature; MODIFIER silent_mutation Average:53.09; most accessible tissue: Callus, score: 93.836 N N N N
vg0112495464 G -> A LOC_Os01g22230.2 upstream_gene_variant ; 4459.0bp to feature; MODIFIER silent_mutation Average:53.09; most accessible tissue: Callus, score: 93.836 N N N N
vg0112495464 G -> A LOC_Os01g22220-LOC_Os01g22230 intergenic_region ; MODIFIER silent_mutation Average:53.09; most accessible tissue: Callus, score: 93.836 N N N N
vg0112495464 G -> DEL N N silent_mutation Average:53.09; most accessible tissue: Callus, score: 93.836 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)
vg0112495464 G A 0.02 0.02 0.02 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0112495464 NA 6.89E-14 mr1062 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
vg0112495464 NA 1.70E-18 mr1242 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
vg0112495464 NA 1.84E-12 mr1553 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
vg0112495464 NA 3.19E-08 mr1648 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
vg0112495464 NA 2.38E-06 mr1695 Jap_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
vg0112495464 NA 1.09E-06 mr1781 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
vg0112495464 NA 3.84E-22 mr1010_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
vg0112495464 NA 5.53E-06 mr1020_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
vg0112495464 NA 1.87E-13 mr1035_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
vg0112495464 NA 2.06E-07 mr1321_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
vg0112495464 NA 6.76E-09 mr1335_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
vg0112495464 NA 4.68E-08 mr1380_2 Jap_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
vg0112495464 4.82E-06 1.52E-07 mr1561_2 Jap_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
vg0112495464 NA 3.95E-17 mr1712_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
vg0112495464 NA 3.54E-06 mr1875_2 Jap_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
vg0112495464 3.08E-06 3.08E-06 mr1908_2 Jap_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
vg0112495464 NA 7.71E-07 mr1996_2 Jap_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