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Detailed information for vg0106670061:

Variant ID: vg0106670061 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6670061
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.10, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATAGTGGACTAAAGCATTTAGCGGAGTTATAGCAGCTAAATTGTATATGAGAATAAATAATTAAAACACTTCTCAAACAGCAACAGCGAAAGATAGC[A/G]
GCTATAACAGAAGATTTAAAACCCTGCTAATAATTTCACTGGGTAATACTAACCAGGAGCAGAGAGGGGGCAAAAGGGACATTTTACATGTAGGAGTGGG

Reverse complement sequence

CCCACTCCTACATGTAAAATGTCCCTTTTGCCCCCTCTCTGCTCCTGGTTAGTATTACCCAGTGAAATTATTAGCAGGGTTTTAAATCTTCTGTTATAGC[T/C]
GCTATCTTTCGCTGTTGCTGTTTGAGAAGTGTTTTAATTATTTATTCTCATATACAATTTAGCTGCTATAACTCCGCTAAATGCTTTAGTCCACTATTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.20% 41.60% 0.19% 0.00% NA
All Indica  2759 79.70% 20.20% 0.11% 0.00% NA
All Japonica  1512 30.90% 68.90% 0.20% 0.00% NA
Aus  269 3.30% 96.70% 0.00% 0.00% NA
Indica I  595 88.40% 11.60% 0.00% 0.00% NA
Indica II  465 68.00% 32.00% 0.00% 0.00% NA
Indica III  913 91.60% 8.40% 0.00% 0.00% NA
Indica Intermediate  786 66.20% 33.50% 0.38% 0.00% NA
Temperate Japonica  767 29.90% 70.10% 0.00% 0.00% NA
Tropical Japonica  504 34.30% 65.30% 0.40% 0.00% NA
Japonica Intermediate  241 27.00% 72.60% 0.41% 0.00% NA
VI/Aromatic  96 26.00% 74.00% 0.00% 0.00% NA
Intermediate  90 58.90% 37.80% 3.33% 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
vg0106670061 A -> G LOC_Os01g12220.1 downstream_gene_variant ; 4601.0bp to feature; MODIFIER silent_mutation Average:93.891; most accessible tissue: Zhenshan97 panicle, score: 97.816 N N N N
vg0106670061 A -> G LOC_Os01g12230.1 intron_variant ; MODIFIER silent_mutation Average:93.891; most accessible tissue: Zhenshan97 panicle, score: 97.816 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)
vg0106670061 A G 0.03 0.03 0.02 0.02 0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106670061 NA 8.51E-09 mr1498 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
vg0106670061 NA 5.78E-06 mr1708 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
vg0106670061 1.70E-11 NA mr1769 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
vg0106670061 5.69E-06 8.79E-13 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
vg0106670061 5.06E-06 NA mr1769 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
vg0106670061 8.42E-06 NA mr1951 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
vg0106670061 8.60E-07 1.61E-10 mr1951 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
vg0106670061 NA 1.81E-07 mr1310_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
vg0106670061 NA 1.67E-07 mr1498_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
vg0106670061 6.43E-07 NA mr1769_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
vg0106670061 NA 7.53E-14 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
vg0106670061 NA 7.05E-07 mr1951_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