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Detailed information for vg0205477779:

Variant ID: vg0205477779 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5477779
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGGACTTTTGAAACAGATACTGCTCATTCCGTTTTATATTATAAAGCGTTTTGATTTTTTTTAAAATTTAAACTTTTTTAAGTTTGATTAAATTCGT[A/T]
AAAAAAATATAGTAACAAACCTAAAGAATTTTGATTTAAAAAATCAAAACAAATTGTAATATGAGATGGATGGAGAGCATATGACATTTCTTCGCCGATC

Reverse complement sequence

GATCGGCGAAGAAATGTCATATGCTCTCCATCCATCTCATATTACAATTTGTTTTGATTTTTTAAATCAAAATTCTTTAGGTTTGTTACTATATTTTTTT[T/A]
ACGAATTTAATCAAACTTAAAAAAGTTTAAATTTTAAAAAAAATCAAAACGCTTTATAATATAAAACGGAATGAGCAGTATCTGTTTCAAAAGTCCATCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 7.00% 0.11% 1.88% NA
All Indica  2759 84.90% 11.80% 0.18% 3.15% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.60% 0.20% 0.00% 2.18% NA
Indica II  465 82.80% 14.80% 0.65% 1.72% NA
Indica III  913 78.10% 17.20% 0.11% 4.60% NA
Indica Intermediate  786 84.40% 12.50% 0.13% 3.05% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0205477779 A -> T LOC_Os02g10400.1 upstream_gene_variant ; 2645.0bp to feature; MODIFIER silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg0205477779 A -> T LOC_Os02g10410.1 upstream_gene_variant ; 1821.0bp to feature; MODIFIER silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg0205477779 A -> T LOC_Os02g10440.1 upstream_gene_variant ; 4949.0bp to feature; MODIFIER silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg0205477779 A -> T LOC_Os02g10430.1 downstream_gene_variant ; 919.0bp to feature; MODIFIER silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg0205477779 A -> T LOC_Os02g10430.2 downstream_gene_variant ; 919.0bp to feature; MODIFIER silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg0205477779 A -> T LOC_Os02g10420.1 intron_variant ; MODIFIER silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 N N N N
vg0205477779 A -> DEL N N silent_mutation Average:57.558; most accessible tissue: Minghui63 flower, score: 88.423 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)
vg0205477779 A T -0.01 -0.01 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205477779 NA 7.84E-06 mr1169_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
vg0205477779 NA 5.41E-07 mr1705_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
vg0205477779 NA 5.10E-07 mr1842_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