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Detailed information for vg0409069254:

Variant ID: vg0409069254 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9069254
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


ACGTGGGTTTGGGGGCGGCCCGACCCCAAGCTGGGAGGGGGCAGCCGCCACAACACCCCGGGCTCAACCCTCCTCAGGGAGAGCCACGTGGGTTTGAGGG[C/T]
GGCCTCCTCCCTCTAGCTGGGTGGGGGTAGCCACCGCTCCACCCCGGGCTTGATCCCCCCTCGTGGGGAGCCACGTAGATTTGGGGGCGGCCTCCTCCCT

Reverse complement sequence

AGGGAGGAGGCCGCCCCCAAATCTACGTGGCTCCCCACGAGGGGGGATCAAGCCCGGGGTGGAGCGGTGGCTACCCCCACCCAGCTAGAGGGAGGAGGCC[G/A]
CCCTCAAACCCACGTGGCTCTCCCTGAGGAGGGTTGAGCCCGGGGTGTTGTGGCGGCTGCCCCCTCCCAGCTTGGGGTCGGGCCGCCCCCAAACCCACGT

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 72.80% 26.60% 0.25% 0.36% NA
All Indica  2759 53.80% 45.20% 0.43% 0.62% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 24.90% 74.80% 0.34% 0.00% NA
Indica II  465 74.80% 23.90% 0.86% 0.43% NA
Indica III  913 59.10% 40.10% 0.11% 0.66% NA
Indica Intermediate  786 56.90% 41.30% 0.64% 1.15% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0409069254 C -> DEL N N silent_mutation Average:78.736; most accessible tissue: Zhenshan97 flag leaf, score: 96.578 N N N N
vg0409069254 C -> T LOC_Os04g16660.1 downstream_gene_variant ; 4786.0bp to feature; MODIFIER silent_mutation Average:78.736; most accessible tissue: Zhenshan97 flag leaf, score: 96.578 N N N N
vg0409069254 C -> T LOC_Os04g16670.1 downstream_gene_variant ; 2770.0bp to feature; MODIFIER silent_mutation Average:78.736; most accessible tissue: Zhenshan97 flag leaf, score: 96.578 N N N N
vg0409069254 C -> T LOC_Os04g16660-LOC_Os04g16670 intergenic_region ; MODIFIER silent_mutation Average:78.736; most accessible tissue: Zhenshan97 flag leaf, score: 96.578 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)
vg0409069254 C T 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0409069254 NA 4.61E-12 mr1403 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
vg0409069254 NA 1.05E-09 mr1403 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
vg0409069254 NA 3.99E-06 mr1830 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
vg0409069254 6.38E-06 NA mr1846 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
vg0409069254 NA 8.69E-11 mr1846 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
vg0409069254 NA 9.37E-10 mr1830_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
vg0409069254 5.36E-09 3.34E-14 mr1846_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
vg0409069254 2.21E-07 2.04E-23 mr1846_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