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Detailed information for vg0824240876:

Variant ID: vg0824240876 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24240876
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCAACCACAGGTGGGAATGGCTGCATCAACCCAGGGAATGGCCCTGCCCCTGGTGCACCAGGGAATCCACCAAACCCAGCACCCATCCTTCCCATTGC[A/G]
CCATAACCAGTAGGATCAAAAGCCTGCCCCATCATTCCGCCTGGAGGCAGCATTGGAGGTGGTGGTGCAACCATTCCACCATTTCCCATGATCCCTCGGC

Reverse complement sequence

GCCGAGGGATCATGGGAAATGGTGGAATGGTTGCACCACCACCTCCAATGCTGCCTCCAGGCGGAATGATGGGGCAGGCTTTTGATCCTACTGGTTATGG[T/C]
GCAATGGGAAGGATGGGTGCTGGGTTTGGTGGATTCCCTGGTGCACCAGGGGCAGGGCCATTCCCTGGGTTGATGCAGCCATTCCCACCTGTGGTTGCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.30% 25.70% 1.99% 0.00% NA
All Indica  2759 90.60% 9.40% 0.07% 0.00% NA
All Japonica  1512 54.70% 39.50% 5.82% 0.00% NA
Aus  269 7.80% 92.20% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 79.40% 20.60% 0.00% 0.00% NA
Indica III  913 93.50% 6.50% 0.00% 0.00% NA
Indica Intermediate  786 86.80% 13.00% 0.25% 0.00% NA
Temperate Japonica  767 72.60% 17.50% 9.91% 0.00% NA
Tropical Japonica  504 32.70% 65.90% 1.39% 0.00% NA
Japonica Intermediate  241 43.60% 54.40% 2.07% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 70.00% 25.60% 4.44% 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
vg0824240876 A -> G LOC_Os08g38240.1 synonymous_variant ; p.Gly382Gly; LOW synonymous_codon Average:87.863; most accessible tissue: Zhenshan97 flag leaf, score: 95.731 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)
vg0824240876 A G 0.01 0.02 0.02 0.02 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824240876 NA 8.70E-08 mr1557 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
vg0824240876 NA 7.51E-09 mr1769 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
vg0824240876 NA 1.40E-06 mr1958 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
vg0824240876 NA 7.94E-06 mr1188_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
vg0824240876 NA 8.81E-09 mr1321_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
vg0824240876 NA 1.07E-06 mr1510_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
vg0824240876 NA 3.87E-08 mr1769_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
vg0824240876 3.67E-06 NA mr1807_2 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
vg0824240876 5.52E-06 9.21E-08 mr1807_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