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Detailed information for vg0434330680:

Variant ID: vg0434330680 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34330680
Reference Allele: TAlternative Allele: C,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.08, A: 0.01, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


GGCAATATTGACCCAACAAGCTTGTTATTTGAGAGGATCAGTGATGACGGGAAGCTACTGAGTTGGTTGTACTGCAAGCCTTTACCAGTGGAAGTCGAAT[T/C,A]
CTTCTTGACGAAGGATAATGGGAGGTCTCCTGTTGACGCCTGCCCACTTGAGCCATTACTTGAAATTAAACTCTTCATCTGTGTAAAGGTTGCAGGAAGC

Reverse complement sequence

GCTTCCTGCAACCTTTACACAGATGAAGAGTTTAATTTCAAGTAATGGCTCAAGTGGGCAGGCGTCAACAGGAGACCTCCCATTATCCTTCGTCAAGAAG[A/G,T]
ATTCGACTTCCACTGGTAAAGGCTTGCAGTACAACCAACTCAGTAGCTTCCCGTCATCACTGATCCTCTCAAATAACAAGCTTGTTGGGTCAATATTGCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.10% 45.20% 0.02% 0.59% A: 0.02%
All Indica  2759 90.50% 8.60% 0.04% 0.80% NA
All Japonica  1512 1.30% 98.50% 0.00% 0.20% A: 0.07%
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 98.50% 1.20% 0.00% 0.34% NA
Indica II  465 95.50% 3.40% 0.00% 1.08% NA
Indica III  913 82.50% 16.50% 0.11% 0.88% NA
Indica Intermediate  786 91.00% 8.10% 0.00% 0.89% NA
Temperate Japonica  767 0.40% 99.50% 0.00% 0.00% A: 0.13%
Tropical Japonica  504 2.60% 97.00% 0.00% 0.40% NA
Japonica Intermediate  241 1.20% 98.30% 0.00% 0.41% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 37.80% 58.90% 0.00% 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
vg0434330680 T -> C LOC_Os04g57660.1 missense_variant ; p.Asn484Asp; MODERATE nonsynonymous_codon Average:68.32; most accessible tissue: Minghui63 root, score: 89.944 benign 0.167 DELETERIOUS 0.04
vg0434330680 T -> DEL LOC_Os04g57660.1 N frameshift_variant Average:68.32; most accessible tissue: Minghui63 root, score: 89.944 N N N N
vg0434330680 T -> A LOC_Os04g57660.1 missense_variant ; p.Asn484Tyr; MODERATE nonsynonymous_codon Average:68.32; most accessible tissue: Minghui63 root, score: 89.944 probably damaging 2.451 DELETERIOUS 0.00

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)
vg0434330680 T A -0.01 -0.01 -0.02 0.0 -0.01 -0.01
vg0434330680 T C -0.03 -0.01 -0.03 -0.01 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434330680 NA 1.67E-48 mr1125 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
vg0434330680 7.11E-06 1.73E-06 mr1157 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
vg0434330680 3.26E-06 7.76E-07 mr1328 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
vg0434330680 4.36E-07 1.32E-07 mr1446 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
vg0434330680 NA 8.31E-13 mr1531 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
vg0434330680 NA 1.11E-23 mr1571 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
vg0434330680 NA 3.43E-31 mr1745 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
vg0434330680 NA 7.54E-30 mr1793 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
vg0434330680 NA 6.73E-49 mr1063_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
vg0434330680 NA 5.82E-62 mr1078_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
vg0434330680 NA 1.36E-62 mr1125_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
vg0434330680 NA 4.35E-13 mr1151_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
vg0434330680 NA 5.20E-22 mr1164_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
vg0434330680 NA 2.98E-16 mr1260_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
vg0434330680 NA 6.39E-34 mr1571_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
vg0434330680 NA 2.33E-29 mr1580_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
vg0434330680 NA 9.63E-21 mr1924_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
vg0434330680 NA 3.31E-26 mr1943_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