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Detailed information for vg0522130001:

Variant ID: vg0522130001 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22130001
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, T: 0.10, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGCCTGAAGTGACATCAGACGTCTTTTTTTTTTTTTGTGTGTGTGTGTGGTTTGGTAAAATTGGTAGCCTGAGGTATGAGCAGATAAAACCAGAGGCA[A/T]
AATTTTCAGATATCTATTGTTAGTGCGATTTGTAACTAGGAAATTCAGTAAGAAGGTTCGTTGTTTATATTTATAAGTTAATAACAACGGAAATGCTCAG

Reverse complement sequence

CTGAGCATTTCCGTTGTTATTAACTTATAAATATAAACAACGAACCTTCTTACTGAATTTCCTAGTTACAAATCGCACTAACAATAGATATCTGAAAATT[T/A]
TGCCTCTGGTTTTATCTGCTCATACCTCAGGCTACCAATTTTACCAAACCACACACACACACAAAAAAAAAAAAAGACGTCTGATGTCACTTCAGGCAGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.50% 37.30% 0.04% 0.13% NA
All Indica  2759 98.00% 1.70% 0.07% 0.18% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 68.80% 31.20% 0.00% 0.00% NA
Indica I  595 99.20% 0.50% 0.17% 0.17% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.30% 0.50% 0.00% 0.11% NA
Indica Intermediate  786 95.50% 3.90% 0.13% 0.38% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0522130001 A -> T LOC_Os05g37790.1 upstream_gene_variant ; 370.0bp to feature; MODIFIER silent_mutation Average:68.442; most accessible tissue: Callus, score: 89.795 N N N N
vg0522130001 A -> T LOC_Os05g37780-LOC_Os05g37790 intergenic_region ; MODIFIER silent_mutation Average:68.442; most accessible tissue: Callus, score: 89.795 N N N N
vg0522130001 A -> DEL N N silent_mutation Average:68.442; most accessible tissue: Callus, score: 89.795 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)
vg0522130001 A T 0.02 0.01 0.01 -0.02 0.0 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522130001 NA 7.43E-22 mr1003 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
vg0522130001 NA 7.86E-14 mr1010 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
vg0522130001 3.91E-06 8.69E-14 mr1013 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
vg0522130001 NA 1.11E-21 mr1163 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
vg0522130001 NA 1.20E-08 mr1595 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
vg0522130001 NA 1.74E-20 mr1689 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
vg0522130001 NA 4.45E-89 mr1718 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
vg0522130001 NA 1.99E-52 mr1795 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
vg0522130001 NA 8.02E-39 mr1890 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
vg0522130001 NA 1.86E-20 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
vg0522130001 NA 7.50E-32 mr1037_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
vg0522130001 NA 4.71E-26 mr1051_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
vg0522130001 NA 2.35E-11 mr1377_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
vg0522130001 NA 5.14E-77 mr1671_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
vg0522130001 NA 4.13E-37 mr1689_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
vg0522130001 NA 2.32E-113 mr1718_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
vg0522130001 NA 1.92E-47 mr1721_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
vg0522130001 NA 2.62E-34 mr1888_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