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Detailed information for vg0204458881:

Variant ID: vg0204458881 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4458881
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTCTTGGCGTATGTAGGTTTGTATTGGCTTGTGGCTTTGTGGCGTCTATGTTGTCCGTGTCCCCTCTCCTCTTAGGGGGCCTTGTATTTATACCCATA[G/A]
GTGTCTCCTTATCCAAGTAGAACTAGGAAAACCAATATAGATACAATCCGAGTAGTCCATGTCGTTTCCATGTAGAACTCTAGTCATCCTTCCTTATGCG

Reverse complement sequence

CGCATAAGGAAGGATGACTAGAGTTCTACATGGAAACGACATGGACTACTCGGATTGTATCTATATTGGTTTTCCTAGTTCTACTTGGATAAGGAGACAC[C/T]
TATGGGTATAAATACAAGGCCCCCTAAGAGGAGAGGGGACACGGACAACATAGACGCCACAAAGCCACAAGCCAATACAAACCTACATACGCCAAGACAA

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 72.00% 27.90% 0.04% 0.00% NA
All Indica  2759 75.10% 24.80% 0.07% 0.00% NA
All Japonica  1512 65.30% 34.70% 0.00% 0.00% NA
Aus  269 77.00% 23.00% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 80.40% 19.10% 0.43% 0.00% NA
Indica III  913 56.50% 43.50% 0.00% 0.00% NA
Indica Intermediate  786 78.60% 21.40% 0.00% 0.00% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 20.80% 79.20% 0.00% 0.00% NA
Japonica Intermediate  241 54.80% 45.20% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0204458881 G -> A LOC_Os02g08370.1 upstream_gene_variant ; 1133.0bp to feature; MODIFIER silent_mutation Average:64.843; most accessible tissue: Minghui63 young leaf, score: 78.821 N N N N
vg0204458881 G -> A LOC_Os02g08380.1 upstream_gene_variant ; 1419.0bp to feature; MODIFIER silent_mutation Average:64.843; most accessible tissue: Minghui63 young leaf, score: 78.821 N N N N
vg0204458881 G -> A LOC_Os02g08364.1 downstream_gene_variant ; 4073.0bp to feature; MODIFIER silent_mutation Average:64.843; most accessible tissue: Minghui63 young leaf, score: 78.821 N N N N
vg0204458881 G -> A LOC_Os02g08370-LOC_Os02g08380 intergenic_region ; MODIFIER silent_mutation Average:64.843; most accessible tissue: Minghui63 young leaf, score: 78.821 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)
vg0204458881 G A -0.04 -0.03 -0.03 -0.03 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204458881 NA 8.70E-12 mr1241 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
vg0204458881 NA 9.61E-10 mr1449 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
vg0204458881 5.17E-06 NA mr1735 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
vg0204458881 NA 3.00E-07 mr1090_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
vg0204458881 NA 7.04E-06 mr1211_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
vg0204458881 NA 4.98E-14 mr1241_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
vg0204458881 NA 3.04E-09 mr1642_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
vg0204458881 NA 5.56E-08 mr1808_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
vg0204458881 NA 2.81E-08 mr1952_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