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Detailed information for vg0228811687:

Variant ID: vg0228811687 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28811687
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.24, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCAGCTCTACCATGGAATTCAGGATTCCGACGATGTCAAGTGTTCTCAAGATGAGGGCTTACTGCTGCTAGATTTGAATATCAAAGGAGGAGGATATG[A/G]
CCATCTGTCCTCCAATGCCATGCGAGGCGGCGAATCCGGTCTGAAGATTAGTCAGCACAGGAGGTAAAGATTCAGTAGAATGGCGACCATCTGTAGTTTA

Reverse complement sequence

TAAACTACAGATGGTCGCCATTCTACTGAATCTTTACCTCCTGTGCTGACTAATCTTCAGACCGGATTCGCCGCCTCGCATGGCATTGGAGGACAGATGG[T/C]
CATATCCTCCTCCTTTGATATTCAAATCTAGCAGCAGTAAGCCCTCATCTTGAGAACACTTGACATCGTCGGAATCCTGAATTCCATGGTAGAGCTGAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.90% 46.60% 0.40% 0.08% NA
All Indica  2759 84.60% 14.80% 0.58% 0.11% NA
All Japonica  1512 0.50% 99.40% 0.07% 0.07% NA
Aus  269 50.20% 49.80% 0.00% 0.00% NA
Indica I  595 91.90% 7.20% 0.84% 0.00% NA
Indica II  465 92.90% 6.00% 0.86% 0.22% NA
Indica III  913 82.00% 17.60% 0.11% 0.22% NA
Indica Intermediate  786 77.00% 22.30% 0.76% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 0.60% 99.20% 0.00% 0.20% NA
Japonica Intermediate  241 0.40% 99.20% 0.41% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 28.90% 68.90% 2.22% 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
vg0228811687 A -> G LOC_Os02g47190.1 missense_variant ; p.Asp267Gly; MODERATE nonsynonymous_codon ; D267G Average:78.807; most accessible tissue: Minghui63 flag leaf, score: 94.996 unknown unknown TOLERATED 0.05
vg0228811687 A -> DEL LOC_Os02g47190.1 N frameshift_variant Average:78.807; most accessible tissue: Minghui63 flag leaf, score: 94.996 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)
vg0228811687 A G 0.0 0.03 0.01 0.01 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228811687 NA 3.52E-07 mr1824 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
vg0228811687 NA 3.14E-15 mr1933 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