Search for Variation information by Variation ID:

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

Detailed information for vg0525640125:

Variant ID: vg0525640125 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25640125
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, C: 0.36, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


CCTCTTTTTTTTTTTTTTGGATGCTTGACTGTTAGAGCAAGTTCAATAGTATAGCCTACTACTAGCTTCAATTCAGCTATAACCAATCTAATAGCCAATT[T/C]
ATACAATAGTTGCTTACTATACTATTAATATATGGTCTCACCTATTATACATATACTGCGTCTTGAAGTCCGTGTTGCAGCTGACTACAGATCTGTAGCC

Reverse complement sequence

GGCTACAGATCTGTAGTCAGCTGCAACACGGACTTCAAGACGCAGTATATGTATAATAGGTGAGACCATATATTAATAGTATAGTAAGCAACTATTGTAT[A/G]
AATTGGCTATTAGATTGGTTATAGCTGAATTGAAGCTAGTAGTAGGCTATACTATTGAACTTGCTCTAACAGTCAAGCATCCAAAAAAAAAAAAAAGAGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.80% 33.60% 16.76% 10.79% NA
All Indica  2759 6.50% 47.40% 27.87% 18.19% NA
All Japonica  1512 99.60% 0.10% 0.20% 0.07% NA
Aus  269 2.60% 95.90% 1.12% 0.37% NA
Indica I  595 0.30% 35.30% 51.93% 12.44% NA
Indica II  465 21.70% 37.00% 24.09% 17.20% NA
Indica III  913 3.70% 59.50% 12.49% 24.32% NA
Indica Intermediate  786 5.50% 48.70% 29.77% 16.03% NA
Temperate Japonica  767 99.30% 0.10% 0.39% 0.13% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 54.40% 20.00% 18.89% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0525640125 T -> DEL N N silent_mutation Average:92.886; most accessible tissue: Zhenshan97 young leaf, score: 99.083 N N N N
vg0525640125 T -> C LOC_Os05g44090.1 upstream_gene_variant ; 3213.0bp to feature; MODIFIER silent_mutation Average:92.886; most accessible tissue: Zhenshan97 young leaf, score: 99.083 N N N N
vg0525640125 T -> C LOC_Os05g44100.1 upstream_gene_variant ; 1470.0bp to feature; MODIFIER silent_mutation Average:92.886; most accessible tissue: Zhenshan97 young leaf, score: 99.083 N N N N
vg0525640125 T -> C LOC_Os05g44090-LOC_Os05g44100 intergenic_region ; MODIFIER silent_mutation Average:92.886; most accessible tissue: Zhenshan97 young leaf, score: 99.083 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)
vg0525640125 T C -0.03 -0.03 -0.02 -0.04 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525640125 NA 9.38E-11 mr1281 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
vg0525640125 1.93E-06 1.93E-06 mr1828 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
vg0525640125 NA 1.38E-54 mr1889 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
vg0525640125 NA 5.71E-72 mr1896 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
vg0525640125 NA 3.75E-29 mr1903 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
vg0525640125 NA 8.06E-78 mr1907 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
vg0525640125 NA 2.48E-07 mr1915 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
vg0525640125 NA 2.20E-72 mr1934 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
vg0525640125 NA 3.64E-53 mr1935 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
vg0525640125 NA 1.11E-20 mr1195_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
vg0525640125 NA 3.34E-18 mr1281_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
vg0525640125 NA 2.87E-08 mr1299_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
vg0525640125 NA 6.91E-11 mr1537_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
vg0525640125 NA 1.00E-25 mr1588_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
vg0525640125 NA 8.43E-17 mr1592_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
vg0525640125 NA 1.02E-07 mr1645_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
vg0525640125 NA 2.35E-10 mr1756_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
vg0525640125 NA 1.88E-07 mr1783_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
vg0525640125 NA 6.85E-16 mr1790_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
vg0525640125 1.79E-08 5.38E-73 mr1828_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
vg0525640125 3.02E-09 5.17E-15 mr1828_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
vg0525640125 NA 5.46E-08 mr1837_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
vg0525640125 NA 2.22E-16 mr1842_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
vg0525640125 NA 1.60E-10 mr1907_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
vg0525640125 NA 8.13E-09 mr1915_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
vg0525640125 NA 1.13E-08 mr1934_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
vg0525640125 NA 1.14E-16 mr1938_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
vg0525640125 NA 2.26E-09 mr1947_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