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Detailed information for vg0603996692:

Variant ID: vg0603996692 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 3996692
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GGGGGGATGGGAACGAAATCCACTGGGCAGAATGGAATTATTGGGGCTCATTCGTCTACCCTGTCTGACGGGACCACTGATCTACCGAGGATTCACAATT[C/T]
CGACGAAAACCGATAAAATTCTGTGAAATTTTAACGTTTTGATATGGCTCGAAATTAGGTTTTGATTGGAATTTCGGAGGTTATACAGTAGATTTGATCA

Reverse complement sequence

TGATCAAATCTACTGTATAACCTCCGAAATTCCAATCAAAACCTAATTTCGAGCCATATCAAAACGTTAAAATTTCACAGAATTTTATCGGTTTTCGTCG[G/A]
AATTGTGAATCCTCGGTAGATCAGTGGTCCCGTCAGACAGGGTAGACGAATGAGCCCCAATAATTCCATTCTGCCCAGTGGATTTCGTTCCCATCCCCCC

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 89.10% 9.00% 1.88% 0.00% NA
All Indica  2759 81.70% 15.30% 3.08% 0.00% NA
All Japonica  1512 99.70% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.70% 6.60% 5.71% 0.00% NA
Indica II  465 57.60% 38.30% 4.09% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 73.80% 22.10% 4.07% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 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 93.30% 4.40% 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
vg0603996692 C -> T LOC_Os06g08240.1 upstream_gene_variant ; 3658.0bp to feature; MODIFIER silent_mutation Average:96.58; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg0603996692 C -> T LOC_Os06g08250.1 upstream_gene_variant ; 533.0bp to feature; MODIFIER silent_mutation Average:96.58; most accessible tissue: Minghui63 panicle, score: 97.671 N N N N
vg0603996692 C -> T LOC_Os06g08250-LOC_Os06g08270 intergenic_region ; MODIFIER silent_mutation Average:96.58; 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)
vg0603996692 C T -0.07 -0.07 -0.04 -0.06 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0603996692 6.38E-06 NA mr1916 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
vg0603996692 1.43E-06 1.43E-06 mr1916 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