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Detailed information for vg0225272821:

Variant ID: vg0225272821 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25272821
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAATCATCGCGCGAGGAGAGGAGAGGAGAGGAAGGATTGCTCACAGCTCAGAGATCATATGATTGGTGATGAAACGAAACCAAGCTGAGGTAAGGCCT[T/A]
AGTGCTGAAGTGCCCGAGTGAAAAGCTGGCTGGAGGAACGAACTGGATATCAGAAGGTTTGTGTTTGTTCGTTGGCTGGCTCGATCACTCGGAGCTCCTG

Reverse complement sequence

CAGGAGCTCCGAGTGATCGAGCCAGCCAACGAACAAACACAAACCTTCTGATATCCAGTTCGTTCCTCCAGCCAGCTTTTCACTCGGGCACTTCAGCACT[A/T]
AGGCCTTACCTCAGCTTGGTTTCGTTTCATCACCAATCATATGATCTCTGAGCTGTGAGCAATCCTTCCTCTCCTCTCCTCTCCTCGCGCGATGATTGCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.50% 25.10% 0.13% 0.28% NA
All Indica  2759 83.70% 15.80% 0.14% 0.36% NA
All Japonica  1512 53.40% 46.40% 0.13% 0.13% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 79.20% 19.80% 0.34% 0.67% NA
Indica II  465 76.30% 23.70% 0.00% 0.00% NA
Indica III  913 94.60% 5.10% 0.00% 0.22% NA
Indica Intermediate  786 78.60% 20.60% 0.25% 0.51% NA
Temperate Japonica  767 34.90% 64.90% 0.13% 0.00% NA
Tropical Japonica  504 77.20% 22.20% 0.20% 0.40% NA
Japonica Intermediate  241 62.20% 37.80% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 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
vg0225272821 T -> A LOC_Os02g42040.1 downstream_gene_variant ; 223.0bp to feature; MODIFIER silent_mutation Average:93.683; most accessible tissue: Callus, score: 98.415 N N N N
vg0225272821 T -> A LOC_Os02g42030-LOC_Os02g42040 intergenic_region ; MODIFIER silent_mutation Average:93.683; most accessible tissue: Callus, score: 98.415 N N N N
vg0225272821 T -> DEL N N silent_mutation Average:93.683; most accessible tissue: Callus, score: 98.415 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)
vg0225272821 T A 0.02 0.01 -0.03 -0.03 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225272821 NA 2.77E-06 mr1164 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
vg0225272821 1.86E-07 1.86E-07 mr1193 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
vg0225272821 NA 7.56E-06 mr1202 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
vg0225272821 NA 2.59E-06 mr1236 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
vg0225272821 NA 1.40E-07 mr1252 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
vg0225272821 NA 7.94E-06 mr1292 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
vg0225272821 NA 3.81E-06 mr1295 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
vg0225272821 2.54E-06 2.53E-06 mr1385 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
vg0225272821 4.96E-06 4.96E-06 mr1421 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
vg0225272821 6.31E-06 6.31E-06 mr1445 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
vg0225272821 4.85E-06 4.85E-06 mr1472 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
vg0225272821 NA 1.77E-06 mr1521 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
vg0225272821 NA 2.75E-06 mr1548 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
vg0225272821 5.61E-06 5.61E-06 mr1630 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
vg0225272821 NA 5.77E-06 mr1737 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
vg0225272821 NA 3.38E-06 mr1741 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
vg0225272821 NA 9.65E-06 mr1748 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
vg0225272821 7.39E-08 7.39E-08 mr1761 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
vg0225272821 NA 9.81E-06 mr1794 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
vg0225272821 8.73E-06 8.72E-06 mr1815 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
vg0225272821 NA 2.63E-08 mr1864 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
vg0225272821 NA 2.13E-06 mr1875 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
vg0225272821 9.47E-06 5.19E-06 mr1941 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
vg0225272821 7.31E-06 7.31E-06 mr1941 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
vg0225272821 NA 8.27E-06 mr1982 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
vg0225272821 NA 6.16E-06 mr1233_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
vg0225272821 9.14E-06 9.13E-06 mr1416_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
vg0225272821 NA 8.65E-06 mr1715_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