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Detailed information for vg0200779191:

Variant ID: vg0200779191 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 779191
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, G: 0.13, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CATCCACGACGAGAAGACTAGTAGTACTACTAATGTGTGCATCTATGTGGATGACAAGGGTTTCCTAAACCGGCGCCGCGCGGTAACAGTAAAAAACCGT[A/G]
CAAAATTTATTAAAAATTTAAATTATTTTTTAAATTTATTTAAATTTAAGGAGGTTACCGTGGTATTGTATTACCGTACCTCGCGGTAAGGCCGGTAACC

Reverse complement sequence

GGTTACCGGCCTTACCGCGAGGTACGGTAATACAATACCACGGTAACCTCCTTAAATTTAAATAAATTTAAAAAATAATTTAAATTTTTAATAAATTTTG[T/C]
ACGGTTTTTTACTGTTACCGCGCGGCGCCGGTTTAGGAAACCCTTGTCATCCACATAGATGCACACATTAGTAGTACTACTAGTCTTCTCGTCGTGGATG

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 62.80% 37.00% 0.25% 0.00% NA
All Indica  2759 93.70% 6.00% 0.33% 0.00% NA
All Japonica  1512 5.90% 94.10% 0.00% 0.00% NA
Aus  269 63.20% 35.70% 1.12% 0.00% NA
Indica I  595 99.00% 0.80% 0.17% 0.00% NA
Indica II  465 78.50% 20.60% 0.86% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 92.50% 7.00% 0.51% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 10.10% 89.90% 0.00% 0.00% NA
Japonica Intermediate  241 13.70% 86.30% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 0.00% 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
vg0200779191 A -> G LOC_Os02g02340.1 upstream_gene_variant ; 835.0bp to feature; MODIFIER silent_mutation Average:93.083; most accessible tissue: Zhenshan97 flower, score: 98.087 N N N N
vg0200779191 A -> G LOC_Os02g02330.1 downstream_gene_variant ; 4009.0bp to feature; MODIFIER silent_mutation Average:93.083; most accessible tissue: Zhenshan97 flower, score: 98.087 N N N N
vg0200779191 A -> G LOC_Os02g02350.1 downstream_gene_variant ; 1451.0bp to feature; MODIFIER silent_mutation Average:93.083; most accessible tissue: Zhenshan97 flower, score: 98.087 N N N N
vg0200779191 A -> G LOC_Os02g02350.3 downstream_gene_variant ; 1451.0bp to feature; MODIFIER silent_mutation Average:93.083; most accessible tissue: Zhenshan97 flower, score: 98.087 N N N N
vg0200779191 A -> G LOC_Os02g02350.2 downstream_gene_variant ; 1451.0bp to feature; MODIFIER silent_mutation Average:93.083; most accessible tissue: Zhenshan97 flower, score: 98.087 N N N N
vg0200779191 A -> G LOC_Os02g02340-LOC_Os02g02350 intergenic_region ; MODIFIER silent_mutation Average:93.083; most accessible tissue: Zhenshan97 flower, score: 98.087 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)
vg0200779191 A G 0.01 -0.03 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200779191 NA 7.75E-34 mr1638 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
vg0200779191 NA 2.54E-09 mr1680 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
vg0200779191 NA 2.53E-21 mr1698 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
vg0200779191 NA 6.51E-06 mr1771 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
vg0200779191 NA 2.83E-06 mr1871_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
vg0200779191 NA 2.01E-06 mr1928_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