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Detailed information for vg0825638880:

Variant ID: vg0825638880 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25638880
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCCATCCATCCTGTGACAGGGTCACAGATCAAGAGTACTGGAACAGATGAGCTGGCCTGTATTTTTCTTTGGTTGGACGCATTGAATTGCAGACCAAATT[T/C]
GAGACAATTTAGGACAGGAGATCTAACATGGTGATTGCTGGAAGACAGATAAGGAGATAAGTGGGGGACAAAGCAGAGGAGAGGATATGGACCATGATCA

Reverse complement sequence

TGATCATGGTCCATATCCTCTCCTCTGCTTTGTCCCCCACTTATCTCCTTATCTGTCTTCCAGCAATCACCATGTTAGATCTCCTGTCCTAAATTGTCTC[A/G]
AATTTGGTCTGCAATTCAATGCGTCCAACCAAAGAAAAATACAGGCCAGCTCATCTGTTCCAGTACTCTTGATCTGTGACCCTGTCACAGGATGGATGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.90% 38.70% 0.17% 0.28% NA
All Indica  2759 36.00% 63.40% 0.18% 0.43% NA
All Japonica  1512 97.30% 2.60% 0.07% 0.07% NA
Aus  269 98.10% 1.50% 0.37% 0.00% NA
Indica I  595 45.50% 53.90% 0.34% 0.17% NA
Indica II  465 28.20% 71.40% 0.00% 0.43% NA
Indica III  913 35.60% 64.10% 0.11% 0.22% NA
Indica Intermediate  786 34.00% 64.90% 0.25% 0.89% NA
Temperate Japonica  767 98.00% 1.80% 0.00% 0.13% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 1.11% 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
vg0825638880 T -> C LOC_Os08g40510.1 upstream_gene_variant ; 4730.0bp to feature; MODIFIER silent_mutation Average:94.056; most accessible tissue: Zhenshan97 root, score: 97.872 N N N N
vg0825638880 T -> C LOC_Os08g40500-LOC_Os08g40510 intergenic_region ; MODIFIER silent_mutation Average:94.056; most accessible tissue: Zhenshan97 root, score: 97.872 N N N N
vg0825638880 T -> DEL N N silent_mutation Average:94.056; most accessible tissue: Zhenshan97 root, score: 97.872 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)
vg0825638880 T C -0.01 0.02 0.02 0.01 0.01 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825638880 4.80E-07 NA mr1874 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
vg0825638880 9.39E-08 7.70E-12 mr1874 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
vg0825638880 1.73E-08 NA mr1874_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
vg0825638880 5.27E-08 1.38E-13 mr1874_2 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