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Detailed information for vg0208973550:

Variant ID: vg0208973550 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8973550
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CAAACACTAAAACTCGATAATTATTCGGTGTATTATGCGAGCACGCTCAATTTGGACCATCCATTTTCAATCCAACGGCGCGCGATCGCCACACATAGCG[A/T]
GTAGCACCACCTCCTCTTTATGGACACCACATTTTTCCTCTCCTATAAATACCCCTCCACACATGAGCAGCCTCTTGCAACCATCAACAAGATACACCAA

Reverse complement sequence

TTGGTGTATCTTGTTGATGGTTGCAAGAGGCTGCTCATGTGTGGAGGGGTATTTATAGGAGAGGAAAAATGTGGTGTCCATAAAGAGGAGGTGGTGCTAC[T/A]
CGCTATGTGTGGCGATCGCGCGCCGTTGGATTGAAAATGGATGGTCCAAATTGAGCGTGCTCGCATAATACACCGAATAATTATCGAGTTTTAGTGTTTG

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 65.10% 16.30% 18.60% 0.00% NA
All Indica  2759 44.00% 26.20% 29.79% 0.00% NA
All Japonica  1512 97.80% 1.20% 0.99% 0.00% NA
Aus  269 84.40% 7.10% 8.55% 0.00% NA
Indica I  595 75.10% 11.10% 13.78% 0.00% NA
Indica II  465 25.40% 33.30% 41.29% 0.00% NA
Indica III  913 28.70% 35.80% 35.49% 0.00% NA
Indica Intermediate  786 49.10% 22.40% 28.50% 0.00% NA
Temperate Japonica  767 98.20% 1.00% 0.78% 0.00% NA
Tropical Japonica  504 96.80% 1.60% 1.59% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 68.90% 10.00% 21.11% 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
vg0208973550 A -> T LOC_Os02g15860.1 upstream_gene_variant ; 182.0bp to feature; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 N N N N
vg0208973550 A -> T LOC_Os02g15870.2 downstream_gene_variant ; 3215.0bp to feature; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 N N N N
vg0208973550 A -> T LOC_Os02g15870.3 downstream_gene_variant ; 3225.0bp to feature; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 N N N N
vg0208973550 A -> T LOC_Os02g15870.4 downstream_gene_variant ; 3225.0bp to feature; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 N N N N
vg0208973550 A -> T LOC_Os02g15870.5 downstream_gene_variant ; 3225.0bp to feature; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 N N N N
vg0208973550 A -> T LOC_Os02g15870.1 downstream_gene_variant ; 4984.0bp to feature; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 N N N N
vg0208973550 A -> T LOC_Os02g15850-LOC_Os02g15860 intergenic_region ; MODIFIER silent_mutation Average:93.075; most accessible tissue: Callus, score: 98.49 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)
vg0208973550 A T 0.06 -0.03 -0.08 0.01 0.03 0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208973550 3.77E-06 3.77E-06 mr1473 Ind_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
vg0208973550 NA 9.65E-06 mr1439_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
vg0208973550 NA 8.78E-06 mr1449_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
vg0208973550 9.87E-06 9.85E-06 mr1473_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
vg0208973550 7.24E-06 7.23E-06 mr1630_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
vg0208973550 NA 2.16E-07 mr1836_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