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Detailed information for vg0316321682:

Variant ID: vg0316321682 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16321682
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CCCATGTGGCTGGGTTCCAATTGAAATGGTTGCTTGAACTTGGAGAATCGAAAGTGACACTTTGGATCTCGATTGAATCCCCTTAATTGCCTCCTCATAT[T/A]
GTACAGCCCACGACAAATAATGCTGCAAATATCTGCACCAACCGAGCTGTATCAATTGGGCTTGGACAGCGACAGACCGAGAGAAAGAAATTAGAGCCCA

Reverse complement sequence

TGGGCTCTAATTTCTTTCTCTCGGTCTGTCGCTGTCCAAGCCCAATTGATACAGCTCGGTTGGTGCAGATATTTGCAGCATTATTTGTCGTGGGCTGTAC[A/T]
ATATGAGGAGGCAATTAAGGGGATTCAATCGAGATCCAAAGTGTCACTTTCGATTCTCCAAGTTCAAGCAACCATTTCAATTGGAACCCAGCCACATGGG

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 67.20% 32.80% 0.02% 0.00% NA
All Indica  2759 85.00% 15.00% 0.04% 0.00% NA
All Japonica  1512 39.00% 61.00% 0.00% 0.00% NA
Aus  269 58.00% 42.00% 0.00% 0.00% NA
Indica I  595 62.50% 37.50% 0.00% 0.00% NA
Indica II  465 95.70% 4.10% 0.22% 0.00% NA
Indica III  913 94.30% 5.70% 0.00% 0.00% NA
Indica Intermediate  786 84.90% 15.10% 0.00% 0.00% NA
Temperate Japonica  767 8.90% 91.10% 0.00% 0.00% NA
Tropical Japonica  504 71.60% 28.40% 0.00% 0.00% NA
Japonica Intermediate  241 66.40% 33.60% 0.00% 0.00% NA
VI/Aromatic  96 19.80% 80.20% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg0316321682 T -> A LOC_Os03g28330-LOC_Os03g28350 intergenic_region ; MODIFIER silent_mutation Average:93.214; most accessible tissue: Zhenshan97 young leaf, score: 99.307 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)
vg0316321682 T A 0.03 0.03 0.0 0.01 0.05 0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316321682 NA 4.98E-06 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0316321682 NA 2.25E-08 mr1063 Jap_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
vg0316321682 NA 2.69E-07 mr1045_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
vg0316321682 NA 1.70E-06 mr1542_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
vg0316321682 5.56E-06 NA mr1789_2 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