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Detailed information for vg0129469514:

Variant ID: vg0129469514 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29469514
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.18, others allele: 0.00, population size: 132. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCCCAGCTTTTCTTCTCCTTGCTTTTGATCTGCCTGCCCTTAGATGTAGCGGAATGGCATGCATGCAGTTGGCGTATTTGCTCATTTGCTCTCTCTCT[T/C]
CCTCTCCTCTCTTCTTTATAATAACCATGTAACTACTGAAAAGCTCGAGTAGTTCTGGCCGGTATTACTACTGCCGGCAGTGTGAAGAAGAGGATATCAA

Reverse complement sequence

TTGATATCCTCTTCTTCACACTGCCGGCAGTAGTAATACCGGCCAGAACTACTCGAGCTTTTCAGTAGTTACATGGTTATTATAAAGAAGAGAGGAGAGG[A/G]
AGAGAGAGAGCAAATGAGCAAATACGCCAACTGCATGCATGCCATTCCGCTACATCTAAGGGCAGGCAGATCAAAAGCAAGGAGAAGAAAAGCTGGGCCT

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 50.60% 22.10% 1.65% 25.60% NA
All Indica  2759 79.80% 0.10% 0.91% 19.21% NA
All Japonica  1512 9.50% 67.30% 2.84% 20.44% NA
Aus  269 6.30% 0.70% 0.74% 92.19% NA
Indica I  595 60.70% 0.00% 1.85% 37.48% NA
Indica II  465 98.10% 0.20% 0.22% 1.51% NA
Indica III  913 83.70% 0.00% 0.44% 15.88% NA
Indica Intermediate  786 79.00% 0.10% 1.15% 19.72% NA
Temperate Japonica  767 0.30% 99.00% 0.26% 0.52% NA
Tropical Japonica  504 27.00% 9.70% 8.13% 55.16% NA
Japonica Intermediate  241 2.10% 86.70% 0.00% 11.20% NA
VI/Aromatic  96 2.10% 1.00% 1.04% 95.83% NA
Intermediate  90 32.20% 25.60% 7.78% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0129469514 T -> DEL N N silent_mutation Average:83.667; most accessible tissue: Minghui63 flower, score: 95.286 N N N N
vg0129469514 T -> C LOC_Os01g51260.1 upstream_gene_variant ; 51.0bp to feature; MODIFIER silent_mutation Average:83.667; most accessible tissue: Minghui63 flower, score: 95.286 N N N N
vg0129469514 T -> C LOC_Os01g51250-LOC_Os01g51260 intergenic_region ; MODIFIER silent_mutation Average:83.667; most accessible tissue: Minghui63 flower, score: 95.286 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)
vg0129469514 T C 0.01 0.0 0.0 0.07 0.04 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129469514 NA 4.69E-13 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
vg0129469514 NA 7.08E-06 mr1011 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
vg0129469514 NA 6.54E-13 mr1056 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
vg0129469514 NA 2.54E-22 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
vg0129469514 NA 6.17E-06 mr1277 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
vg0129469514 NA 6.97E-10 mr1581 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
vg0129469514 NA 1.10E-12 mr1217_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
vg0129469514 NA 4.97E-06 mr1296_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
vg0129469514 NA 1.30E-07 mr1302_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
vg0129469514 3.23E-06 1.42E-08 mr1358_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
vg0129469514 NA 2.08E-06 mr1364_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
vg0129469514 NA 1.55E-07 mr1376_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
vg0129469514 NA 5.82E-08 mr1431_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
vg0129469514 NA 1.52E-06 mr1462_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
vg0129469514 NA 3.60E-06 mr1483_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
vg0129469514 NA 3.82E-09 mr1546_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
vg0129469514 NA 5.65E-21 mr1627_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
vg0129469514 NA 4.38E-08 mr1676_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
vg0129469514 NA 1.06E-07 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
vg0129469514 NA 5.13E-07 mr1807_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
vg0129469514 NA 5.56E-07 mr1824_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
vg0129469514 NA 2.21E-06 mr1836_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
vg0129469514 NA 9.49E-14 mr1838_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
vg0129469514 NA 1.82E-07 mr1882_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
vg0129469514 NA 1.70E-07 mr1899_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
vg0129469514 NA 1.18E-06 mr1971_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
vg0129469514 NA 3.03E-11 mr1986_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