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Detailed information for vg0433338500:

Variant ID: vg0433338500 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33338500
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


AACAAGTGTGTAGATTAATTTGACTGTACTTACTTCCCTACCAACCGCATCTGACTGAGTACTTTTGTCGTCCCAGCAATTCTTTTACCTGTAACTCAGA[A/T]
TGAAGCCGCTCTTCAGTTCAGAGTTCAGACTTTCAGCGTGGCACTCACAGCGCAGTTTTTCGCCGATCGATCGATCGACAGCGCCGTTGAACCGAACACG

Reverse complement sequence

CGTGTTCGGTTCAACGGCGCTGTCGATCGATCGATCGGCGAAAAACTGCGCTGTGAGTGCCACGCTGAAAGTCTGAACTCTGAACTGAAGAGCGGCTTCA[T/A]
TCTGAGTTACAGGTAAAAGAATTGCTGGGACGACAAAAGTACTCAGTCAGATGCGGTTGGTAGGGAAGTAAGTACAGTCAAATTAATCTACACACTTGTT

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 62.00% 37.90% 0.15% 0.00% NA
All Indica  2759 89.40% 10.50% 0.07% 0.00% NA
All Japonica  1512 6.70% 93.00% 0.26% 0.00% NA
Aus  269 84.40% 15.20% 0.37% 0.00% NA
Indica I  595 96.50% 3.40% 0.17% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 79.70% 20.30% 0.00% 0.00% NA
Indica Intermediate  786 91.10% 8.80% 0.13% 0.00% NA
Temperate Japonica  767 6.60% 92.80% 0.52% 0.00% NA
Tropical Japonica  504 6.50% 93.50% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg0433338500 A -> T LOC_Os04g55970.2 upstream_gene_variant ; 3478.0bp to feature; MODIFIER silent_mutation Average:82.014; most accessible tissue: Callus, score: 98.318 N N N N
vg0433338500 A -> T LOC_Os04g55970.1 upstream_gene_variant ; 3478.0bp to feature; MODIFIER silent_mutation Average:82.014; most accessible tissue: Callus, score: 98.318 N N N N
vg0433338500 A -> T LOC_Os04g55960.1 downstream_gene_variant ; 2635.0bp to feature; MODIFIER silent_mutation Average:82.014; most accessible tissue: Callus, score: 98.318 N N N N
vg0433338500 A -> T LOC_Os04g55960-LOC_Os04g55970 intergenic_region ; MODIFIER silent_mutation Average:82.014; most accessible tissue: Callus, score: 98.318 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)
vg0433338500 A T 0.01 -0.01 0.0 -0.01 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433338500 NA 2.39E-10 mr1683 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
vg0433338500 NA 2.16E-14 mr1133_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
vg0433338500 NA 6.50E-19 mr1239_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
vg0433338500 NA 2.06E-23 mr1242_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
vg0433338500 NA 2.37E-13 mr1496_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
vg0433338500 NA 6.45E-14 mr1529_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
vg0433338500 NA 1.03E-08 mr1681_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
vg0433338500 2.16E-06 1.31E-07 mr1699_2 Ind_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
vg0433338500 NA 9.28E-08 mr1765_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
vg0433338500 NA 3.11E-14 mr1936_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