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Detailed information for vg0224821353:

Variant ID: vg0224821353 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24821353
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: 0.06, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTTTGAAAATGGTTTTGTTTTACTAATCAGATGGATATATATTACATATATAAACTTTTTTTCCTCGCAAAAAAAAGTTTATATATGTAATATATATC[C/T]
ATCTGATTTTTTTTAAGTTCTCAAAAAAAATCTGATTTTTTTTATATATATTAATGCCTGCAAGCTTCAAACACATAACTCAAGCTGACACATGGCCAGA

Reverse complement sequence

TCTGGCCATGTGTCAGCTTGAGTTATGTGTTTGAAGCTTGCAGGCATTAATATATATAAAAAAAATCAGATTTTTTTTGAGAACTTAAAAAAAATCAGAT[G/A]
GATATATATTACATATATAAACTTTTTTTTGCGAGGAAAAAAAGTTTATATATGTAATATATATCCATCTGATTAGTAAAACAAAACCATTTTCAAAGAC

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 67.90% 31.90% 0.19% 0.00% NA
All Indica  2759 50.60% 49.20% 0.25% 0.00% NA
All Japonica  1512 97.60% 2.40% 0.00% 0.00% NA
Aus  269 67.70% 32.00% 0.37% 0.00% NA
Indica I  595 60.70% 38.70% 0.67% 0.00% NA
Indica II  465 44.10% 55.90% 0.00% 0.00% NA
Indica III  913 53.20% 46.70% 0.11% 0.00% NA
Indica Intermediate  786 43.60% 56.10% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 93.80% 6.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 6.20% 1.04% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0224821353 C -> T LOC_Os02g41450.1 downstream_gene_variant ; 1535.0bp to feature; MODIFIER silent_mutation Average:77.579; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg0224821353 C -> T LOC_Os02g41450-LOC_Os02g41460 intergenic_region ; MODIFIER silent_mutation Average:77.579; most accessible tissue: Minghui63 panicle, score: 97.671 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)
vg0224821353 C T -0.01 -0.02 -0.02 -0.01 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224821353 5.26E-06 NA mr1101 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
vg0224821353 NA 3.92E-06 mr1561 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
vg0224821353 3.10E-06 NA mr1868 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