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Detailed information for vg0320572496:

Variant ID: vg0320572496 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20572496
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CGCTGAGCTCGGCTACTCCGGCAAGGACGACGTACGCCGTCCGCCACGCTAGCAGCAGCTCCAGGACCAGGCCCAGCTGAGCACTAACGGCACATGCGCT[G/A]
TTGTTAAATTTGTTGTCGTAACTAACACGCATGCATGTATGTAAGACGGGGTGGCAGAATTGGTGTATATATAAAAAGGCTTTGAATAGCAATCCTGTTG

Reverse complement sequence

CAACAGGATTGCTATTCAAAGCCTTTTTATATATACACCAATTCTGCCACCCCGTCTTACATACATGCATGCGTGTTAGTTACGACAACAAATTTAACAA[C/T]
AGCGCATGTGCCGTTAGTGCTCAGCTGGGCCTGGTCCTGGAGCTGCTGCTAGCGTGGCGGACGGCGTACGTCGTCCTTGCCGGAGTAGCCGAGCTCAGCG

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 59.30% 40.00% 0.19% 0.53% NA
All Indica  2759 34.00% 65.10% 0.25% 0.58% NA
All Japonica  1512 98.80% 0.80% 0.00% 0.40% NA
Aus  269 82.50% 17.50% 0.00% 0.00% NA
Indica I  595 46.10% 53.30% 0.17% 0.50% NA
Indica II  465 29.50% 69.70% 0.43% 0.43% NA
Indica III  913 32.20% 67.10% 0.22% 0.44% NA
Indica Intermediate  786 29.80% 69.10% 0.25% 0.89% NA
Temperate Japonica  767 99.50% 0.40% 0.00% 0.13% NA
Tropical Japonica  504 97.80% 1.60% 0.00% 0.60% NA
Japonica Intermediate  241 98.80% 0.40% 0.00% 0.83% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 60.00% 34.40% 2.22% 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
vg0320572496 G -> A LOC_Os03g37120.1 3_prime_UTR_variant ; 49.0bp to feature; MODIFIER silent_mutation Average:83.256; most accessible tissue: Callus, score: 90.133 N N N N
vg0320572496 G -> A LOC_Os03g37110.1 upstream_gene_variant ; 3973.0bp to feature; MODIFIER silent_mutation Average:83.256; most accessible tissue: Callus, score: 90.133 N N N N
vg0320572496 G -> A LOC_Os03g37130.1 downstream_gene_variant ; 1745.0bp to feature; MODIFIER silent_mutation Average:83.256; most accessible tissue: Callus, score: 90.133 N N N N
vg0320572496 G -> DEL N N silent_mutation Average:83.256; most accessible tissue: Callus, score: 90.133 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)
vg0320572496 G A -0.09 -0.03 -0.03 -0.03 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320572496 NA 8.79E-07 mr1221 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
vg0320572496 NA 1.01E-06 mr1439 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
vg0320572496 NA 6.15E-08 mr1624 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
vg0320572496 NA 1.51E-06 mr1735 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
vg0320572496 NA 2.83E-08 mr1785 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
vg0320572496 NA 1.38E-06 mr1378_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