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Detailed information for vg0916034764:

Variant ID: vg0916034764 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16034764
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATGAGAAAATTTGATAAGGCAAAATTAGGCACGTCGGGACCAGGAACAATTAGAGCAATAAAGCTAAAATTAAGCAATCAATAAGGCAACGGCAACGCA[C/T]
GGAGGCAAAAAAAAAAAAAACACTTTTTTTGAATGAAGCCGAGCCAGCAATTGGTGGTGTTTGTATTAAGCTGGAATAAAAATCATGTATACATGTTTCC

Reverse complement sequence

GGAAACATGTATACATGATTTTTATTCCAGCTTAATACAAACACCACCAATTGCTGGCTCGGCTTCATTCAAAAAAAGTGTTTTTTTTTTTTTTGCCTCC[G/A]
TGCGTTGCCGTTGCCTTATTGATTGCTTAATTTTAGCTTTATTGCTCTAATTGTTCCTGGTCCCGACGTGCCTAATTTTGCCTTATCAAATTTTCTCATC

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 41.10% 6.30% 0.19% 52.48% NA
All Indica  2759 8.00% 10.30% 0.33% 81.37% NA
All Japonica  1512 99.30% 0.00% 0.00% 0.66% NA
Aus  269 24.20% 2.60% 0.00% 73.23% NA
Indica I  595 7.40% 33.30% 0.34% 58.99% NA
Indica II  465 10.10% 1.90% 0.22% 87.74% NA
Indica III  913 4.60% 0.50% 0.22% 94.63% NA
Indica Intermediate  786 11.10% 9.30% 0.51% 79.13% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.39% NA
Tropical Japonica  504 98.80% 0.00% 0.00% 1.19% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 1.04% NA
Intermediate  90 66.70% 3.30% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0916034764 C -> DEL N N silent_mutation Average:43.049; most accessible tissue: Minghui63 flower, score: 85.666 N N N N
vg0916034764 C -> T LOC_Os09g26540.1 downstream_gene_variant ; 4078.0bp to feature; MODIFIER silent_mutation Average:43.049; most accessible tissue: Minghui63 flower, score: 85.666 N N N N
vg0916034764 C -> T LOC_Os09g26540.2 downstream_gene_variant ; 4078.0bp to feature; MODIFIER silent_mutation Average:43.049; most accessible tissue: Minghui63 flower, score: 85.666 N N N N
vg0916034764 C -> T LOC_Os09g26530.1 intron_variant ; MODIFIER silent_mutation Average:43.049; most accessible tissue: Minghui63 flower, score: 85.666 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)
vg0916034764 C T 0.0 0.02 0.03 0.01 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916034764 NA 5.30E-06 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
vg0916034764 NA 5.81E-06 mr1052 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
vg0916034764 4.63E-07 9.88E-07 mr1651 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
vg0916034764 4.03E-06 4.03E-06 mr1651 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
vg0916034764 NA 4.38E-19 mr1707 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
vg0916034764 NA 9.92E-12 mr1707 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
vg0916034764 NA 1.10E-21 mr1728 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
vg0916034764 NA 2.75E-14 mr1728 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
vg0916034764 NA 1.41E-14 mr1860 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
vg0916034764 NA 1.10E-10 mr1860 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
vg0916034764 NA 1.66E-15 mr1707_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
vg0916034764 NA 1.93E-09 mr1707_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
vg0916034764 NA 6.32E-20 mr1728_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
vg0916034764 NA 1.17E-11 mr1728_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
vg0916034764 NA 6.16E-14 mr1860_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
vg0916034764 NA 1.01E-10 mr1860_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