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Detailed information for vg0916858916:

Variant ID: vg0916858916 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16858916
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, T: 0.18, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGAGGAGAGAGAGAAGAAGCGGGCTGTAAACTTACAGCCGGCTTGGACACAAGAACCAAGAAACTCTGTGAGAGAGACAAGTGGGCCCTGTATTAATT[G/T]
TAAAGTGCAAACTATTATATGGGTAGGTTGAGAAAATGCTACAAAGAACCTTGTAGCCAACAGGTCGGTTGTATTATTAGCCTTGCTCTAATTATTACTC

Reverse complement sequence

GAGTAATAATTAGAGCAAGGCTAATAATACAACCGACCTGTTGGCTACAAGGTTCTTTGTAGCATTTTCTCAACCTACCCATATAATAGTTTGCACTTTA[C/A]
AATTAATACAGGGCCCACTTGTCTCTCTCACAGAGTTTCTTGGTTCTTGTGTCCAAGCCGGCTGTAAGTTTACAGCCCGCTTCTTCTCTCTCTCCTCTCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.10% 45.80% 0.11% 0.00% NA
All Indica  2759 80.50% 19.50% 0.07% 0.00% NA
All Japonica  1512 1.10% 98.80% 0.13% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 48.60% 51.40% 0.00% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 77.10% 22.60% 0.25% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.60% 0.20% 0.00% NA
Japonica Intermediate  241 3.30% 96.30% 0.41% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 37.80% 61.10% 1.11% 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
vg0916858916 G -> T LOC_Os09g27690.1 downstream_gene_variant ; 4152.0bp to feature; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 N N N N
vg0916858916 G -> T LOC_Os09g27690.5 downstream_gene_variant ; 4152.0bp to feature; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 N N N N
vg0916858916 G -> T LOC_Os09g27690.2 downstream_gene_variant ; 4152.0bp to feature; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 N N N N
vg0916858916 G -> T LOC_Os09g27690.4 downstream_gene_variant ; 4152.0bp to feature; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 N N N N
vg0916858916 G -> T LOC_Os09g27690.6 downstream_gene_variant ; 4152.0bp to feature; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 N N N N
vg0916858916 G -> T LOC_Os09g27700.1 intron_variant ; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 N N N N
vg0916858916 G -> T LOC_Os09g27700.2 intron_variant ; MODIFIER silent_mutation Average:82.909; most accessible tissue: Zhenshan97 root, score: 93.096 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)
vg0916858916 G T -0.01 -0.06 -0.05 -0.03 -0.05 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916858916 NA 7.78E-06 mr1136 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
vg0916858916 NA 6.12E-13 mr1138 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
vg0916858916 1.77E-07 1.18E-13 mr1138 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
vg0916858916 NA 1.69E-06 mr1291 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
vg0916858916 NA 6.39E-09 mr1354 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
vg0916858916 NA 5.70E-10 mr1595 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
vg0916858916 5.84E-06 2.68E-10 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
vg0916858916 1.59E-07 NA 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
vg0916858916 1.48E-08 5.08E-15 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
vg0916858916 NA 3.15E-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
vg0916858916 8.45E-08 7.57E-15 mr1138_2 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
vg0916858916 8.96E-09 8.68E-13 mr1138_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
vg0916858916 NA 6.74E-12 mr1216_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
vg0916858916 NA 3.42E-06 mr1354_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
vg0916858916 NA 5.53E-06 mr1479_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
vg0916858916 NA 7.56E-07 mr1543_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
vg0916858916 NA 4.23E-10 mr1595_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
vg0916858916 NA 3.23E-08 mr1600_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
vg0916858916 NA 1.27E-06 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
vg0916858916 2.74E-06 NA 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
vg0916858916 6.78E-07 2.53E-13 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
vg0916858916 9.61E-06 2.66E-11 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
vg0916858916 NA 1.45E-06 mr1875_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
vg0916858916 NA 1.76E-06 mr1895_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