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Detailed information for vg0623453825:

Variant ID: vg0623453825 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23453825
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCCACTTGCTTTCCTCCCATCCCACCACACGCACGTCGCGCGGCCGGCACACGTACGTCTCTCCGTCTCTCAAACACGCCTACGTACACCGCCACAACC[C/T]
GTGCGTGCGCACGCGCGTGGCATGCATGGGTCCCCGGCCAACTCCCGTCGCTCGACGCGGCCCGATCGAATCGAATCAAAACCCGCACGCACACGAATTC

Reverse complement sequence

GAATTCGTGTGCGTGCGGGTTTTGATTCGATTCGATCGGGCCGCGTCGAGCGACGGGAGTTGGCCGGGGACCCATGCATGCCACGCGCGTGCGCACGCAC[G/A]
GGTTGTGGCGGTGTACGTAGGCGTGTTTGAGAGACGGAGAGACGTACGTGTGCCGGCCGCGCGACGTGCGTGTGGTGGGATGGGAGGAAAGCAAGTGGGC

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 57.10% 9.00% 11.19% 22.75% NA
All Indica  2759 37.80% 8.40% 17.65% 36.10% NA
All Japonica  1512 98.70% 0.30% 0.40% 0.60% NA
Aus  269 3.70% 66.20% 11.52% 18.59% NA
Indica I  595 11.60% 2.20% 26.22% 60.00% NA
Indica II  465 56.60% 9.90% 7.31% 26.24% NA
Indica III  913 40.60% 10.30% 19.28% 29.79% NA
Indica Intermediate  786 43.40% 10.10% 15.39% 31.17% NA
Temperate Japonica  767 98.60% 0.40% 0.26% 0.78% NA
Tropical Japonica  504 99.00% 0.40% 0.60% 0.00% NA
Japonica Intermediate  241 98.30% 0.00% 0.41% 1.24% NA
VI/Aromatic  96 91.70% 4.20% 1.04% 3.12% NA
Intermediate  90 72.20% 4.40% 4.44% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0623453825 C -> T LOC_Os06g39480.1 upstream_gene_variant ; 4372.0bp to feature; MODIFIER silent_mutation Average:90.922; most accessible tissue: Zhenshan97 flower, score: 97.811 N N N N
vg0623453825 C -> T LOC_Os06g39500.1 upstream_gene_variant ; 1645.0bp to feature; MODIFIER silent_mutation Average:90.922; most accessible tissue: Zhenshan97 flower, score: 97.811 N N N N
vg0623453825 C -> T LOC_Os06g39510.1 upstream_gene_variant ; 2761.0bp to feature; MODIFIER silent_mutation Average:90.922; most accessible tissue: Zhenshan97 flower, score: 97.811 N N N N
vg0623453825 C -> T LOC_Os06g39500-LOC_Os06g39510 intergenic_region ; MODIFIER silent_mutation Average:90.922; most accessible tissue: Zhenshan97 flower, score: 97.811 N N N N
vg0623453825 C -> DEL N N silent_mutation Average:90.922; most accessible tissue: Zhenshan97 flower, score: 97.811 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)
vg0623453825 C T -0.08 -0.07 -0.05 0.01 -0.01 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623453825 NA 1.32E-11 mr1006 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
vg0623453825 NA 2.60E-06 mr1006 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
vg0623453825 NA 8.26E-09 mr1007 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
vg0623453825 NA 1.59E-11 mr1052 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
vg0623453825 NA 1.68E-06 mr1052 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
vg0623453825 NA 1.52E-06 mr1073 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
vg0623453825 NA 1.05E-06 mr1556 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
vg0623453825 NA 1.30E-06 mr1847 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
vg0623453825 NA 9.46E-09 mr1004_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
vg0623453825 NA 1.16E-07 mr1006_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
vg0623453825 NA 1.90E-06 mr1006_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