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Detailed information for vg0216347691:

Variant ID: vg0216347691 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16347691
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


CCATATATGATGTAGCATATTTTCAGTCCAATTCTATTATATCCATTTTGCTTTAAAATCAAATAACAAATGGGCCATGTCCATTACAAAAGCCCATATA[G/T]
ACCCAAACATTGGACACACCATTTTCAGCCCATCATATTATATTCATTTATATTAGTATCAAATAACAAGTGTGCTAAGCCCATATAGGCCCAACAATCA

Reverse complement sequence

TGATTGTTGGGCCTATATGGGCTTAGCACACTTGTTATTTGATACTAATATAAATGAATATAATATGATGGGCTGAAAATGGTGTGTCCAATGTTTGGGT[C/A]
TATATGGGCTTTTGTAATGGACATGGCCCATTTGTTATTTGATTTTAAAGCAAAATGGATATAATAGAATTGGACTGAAAATATGCTACATCATATATGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.60% 12.80% 0.61% 40.03% NA
All Indica  2759 20.10% 18.10% 0.80% 61.00% NA
All Japonica  1512 98.80% 0.40% 0.00% 0.79% NA
Aus  269 1.90% 32.70% 2.23% 63.20% NA
Indica I  595 1.70% 22.90% 1.68% 73.78% NA
Indica II  465 16.30% 28.60% 0.86% 54.19% NA
Indica III  913 37.80% 10.50% 0.55% 51.15% NA
Indica Intermediate  786 15.60% 17.20% 0.38% 66.79% NA
Temperate Japonica  767 99.10% 0.00% 0.00% 0.91% NA
Tropical Japonica  504 99.00% 0.60% 0.00% 0.40% NA
Japonica Intermediate  241 97.50% 1.20% 0.00% 1.24% NA
VI/Aromatic  96 95.80% 1.00% 0.00% 3.12% NA
Intermediate  90 62.20% 10.00% 1.11% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0216347691 G -> T LOC_Os02g27594.1 3_prime_UTR_variant ; 292.0bp to feature; MODIFIER silent_mutation Average:63.37; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg0216347691 G -> T LOC_Os02g27592.1 upstream_gene_variant ; 2002.0bp to feature; MODIFIER silent_mutation Average:63.37; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg0216347691 G -> T LOC_Os02g27592.2 upstream_gene_variant ; 2002.0bp to feature; MODIFIER silent_mutation Average:63.37; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg0216347691 G -> T LOC_Os02g27594.2 downstream_gene_variant ; 10.0bp to feature; MODIFIER silent_mutation Average:63.37; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg0216347691 G -> T LOC_Os02g27594.3 downstream_gene_variant ; 10.0bp to feature; MODIFIER silent_mutation Average:63.37; most accessible tissue: Minghui63 young leaf, score: 99.097 N N N N
vg0216347691 G -> DEL N N silent_mutation Average:63.37; most accessible tissue: Minghui63 young leaf, score: 99.097 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)
vg0216347691 G T -0.21 -0.23 -0.15 -0.14 -0.17 -0.19

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216347691 NA 8.80E-10 mr1317 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
vg0216347691 NA 7.03E-12 mr1317 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
vg0216347691 5.26E-07 2.01E-08 mr1350 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
vg0216347691 NA 2.47E-06 mr1818 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
vg0216347691 8.37E-10 6.97E-37 mr1855 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
vg0216347691 3.72E-09 2.21E-25 mr1855 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
vg0216347691 NA 7.81E-08 mr1914 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
vg0216347691 NA 3.95E-06 mr1927 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
vg0216347691 NA 1.70E-06 mr1257_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
vg0216347691 3.97E-06 6.00E-14 mr1317_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
vg0216347691 NA 2.81E-15 mr1317_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
vg0216347691 NA 1.81E-06 mr1559_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
vg0216347691 NA 5.15E-10 mr1608_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
vg0216347691 NA 3.74E-08 mr1608_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
vg0216347691 5.12E-06 NA mr1610_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
vg0216347691 8.42E-07 4.22E-11 mr1610_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
vg0216347691 NA 1.06E-13 mr1818_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
vg0216347691 7.06E-06 2.93E-11 mr1818_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
vg0216347691 5.03E-06 3.25E-40 mr1855_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
vg0216347691 NA 2.51E-29 mr1855_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
vg0216347691 1.53E-06 1.07E-16 mr1897_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
vg0216347691 8.74E-06 2.84E-12 mr1897_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
vg0216347691 2.94E-06 3.35E-13 mr1914_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
vg0216347691 8.67E-06 4.02E-16 mr1914_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
vg0216347691 1.16E-06 NA mr1927_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
vg0216347691 5.40E-06 6.73E-15 mr1927_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