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Detailed information for vg0208715394:

Variant ID: vg0208715394 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8715394
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCGCTGAATGTCGTGCCACCGTGAATAGGAGGCTGAGTCAGCGTGCCAATGTACATTCAGCGTCGTGCTATTTAGCGCTGAGGTGTCTAAGTTTAGTG[C/T]
CATATGATTTGGCGCTGAACAAAATGGTAATTTTTTAAATAAGTTTTGATGACAGTTCATTTGTAAAATTAGTTTTTGTAAAGGGTCGTATTGTCAAAAT

Reverse complement sequence

ATTTTGACAATACGACCCTTTACAAAAACTAATTTTACAAATGAACTGTCATCAAAACTTATTTAAAAAATTACCATTTTGTTCAGCGCCAAATCATATG[G/A]
CACTAAACTTAGACACCTCAGCGCTAAATAGCACGACGCTGAATGTACATTGGCACGCTGACTCAGCCTCCTATTCACGGTGGCACGACATTCAGCGCCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.70% 15.30% 0.02% 0.00% NA
All Indica  2759 81.90% 18.00% 0.04% 0.00% NA
All Japonica  1512 98.70% 1.30% 0.00% 0.00% NA
Aus  269 33.10% 66.90% 0.00% 0.00% NA
Indica I  595 83.00% 17.00% 0.00% 0.00% NA
Indica II  465 77.20% 22.60% 0.22% 0.00% NA
Indica III  913 83.90% 16.10% 0.00% 0.00% NA
Indica Intermediate  786 81.70% 18.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0208715394 C -> T LOC_Os02g15540.1 upstream_gene_variant ; 339.0bp to feature; MODIFIER silent_mutation Average:92.699; most accessible tissue: Minghui63 young leaf, score: 99.299 N N N N
vg0208715394 C -> T LOC_Os02g15540-LOC_Os02g15550 intergenic_region ; MODIFIER silent_mutation Average:92.699; most accessible tissue: Minghui63 young leaf, score: 99.299 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)
vg0208715394 C T -0.01 -0.03 -0.05 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208715394 2.56E-06 2.89E-06 mr1826 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
vg0208715394 NA 6.17E-06 mr1826 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