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Detailed information for vg0134771269:

Variant ID: vg0134771269 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34771269
Reference Allele: TAlternative Allele: A,G
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.03, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCCCACGATGGTTGGTCAGTTCCCATCAGCAGTTAAACGGTACTACACAACAAAGCTGAAGATGGATGGATGGATTAAATTGTTAAAAATATGGGGGG[T/A,G]
AATTACTCATTAGAGCGATTTGGATGCCATTAGGCAAAACCCACTAAAATTAGGGCGTCAAACTTGGGCCAGAGTTTGCATGAGATGCATGCAGCATTGG

Reverse complement sequence

CCAATGCTGCATGCATCTCATGCAAACTCTGGCCCAAGTTTGACGCCCTAATTTTAGTGGGTTTTGCCTAATGGCATCCAAATCGCTCTAATGAGTAATT[A/T,C]
CCCCCCATATTTTTAACAATTTAATCCATCCATCCATCTTCAGCTTTGTTGTGTAGTACCGTTTAACTGCTGATGGGAACTGACCAACCATCGTGGGGAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.00% 44.80% 0.17% 0.00% G: 0.02%
All Indica  2759 28.90% 70.80% 0.29% 0.00% G: 0.04%
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 37.50% 62.20% 0.34% 0.00% NA
Indica II  465 8.60% 91.00% 0.43% 0.00% NA
Indica III  913 26.10% 73.70% 0.22% 0.00% NA
Indica Intermediate  786 37.70% 62.00% 0.25% 0.00% G: 0.13%
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0134771269 T -> G LOC_Os01g60120.2 downstream_gene_variant ; 4856.0bp to feature; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> G LOC_Os01g60120.3 downstream_gene_variant ; 4856.0bp to feature; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> G LOC_Os01g60120.1 downstream_gene_variant ; 4860.0bp to feature; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> G LOC_Os01g60110.1 intron_variant ; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> A LOC_Os01g60120.2 downstream_gene_variant ; 4856.0bp to feature; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> A LOC_Os01g60120.3 downstream_gene_variant ; 4856.0bp to feature; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> A LOC_Os01g60120.1 downstream_gene_variant ; 4860.0bp to feature; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 N N N N
vg0134771269 T -> A LOC_Os01g60110.1 intron_variant ; MODIFIER silent_mutation Average:96.634; most accessible tissue: Zhenshan97 flower, score: 99.337 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)
vg0134771269 T A -0.05 -0.01 0.0 -0.05 -0.02 -0.01
vg0134771269 T G 0.02 0.01 0.02 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134771269 NA 6.45E-10 mr1761 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