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Detailed information for vg0501460647:

Variant ID: vg0501460647 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 1460647
Reference Allele: GAlternative Allele: A,GCTCTAAGC
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGCAGCTGGCTACAGAAATGTAGCCCGCTGCTCTTCTCTTTCATCTTTTATCTTATTAAAATATGTTTACAGCTAGCTAATAGCCTGCTATTGTACCT[G/A,GCTCTAAGC]
CTCTAACTGAAGTGCCAGGTGACTTGCTTGGTTGGTTAAAGATGATACAGATGGAGCAGTAACTTCACAGGATTCTGGTTTCTATTGCCTGTCTATTAGG

Reverse complement sequence

CCTAATAGACAGGCAATAGAAACCAGAATCCTGTGAAGTTACTGCTCCATCTGTATCATCTTTAACCAACCAAGCAAGTCACCTGGCACTTCAGTTAGAG[C/T,GCTTAGAGC]
AGGTACAATAGCAGGCTATTAGCTAGCTGTAAACATATTTTAATAAGATAAAAGATGAAAGAGAAGAGCAGCGGGCTACATTTCTGTAGCCAGCTGCAGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.90% 47.20% 0.13% 0.02% GCTCTAAGC: 3.75%
All Indica  2759 26.80% 72.60% 0.18% 0.04% GCTCTAAGC: 0.43%
All Japonica  1512 89.40% 2.30% 0.00% 0.00% GCTCTAAGC: 8.33%
Aus  269 41.60% 58.00% 0.37% 0.00% NA
Indica I  595 4.70% 95.00% 0.34% 0.00% NA
Indica II  465 47.10% 52.50% 0.22% 0.00% GCTCTAAGC: 0.22%
Indica III  913 30.00% 69.00% 0.11% 0.00% GCTCTAAGC: 0.88%
Indica Intermediate  786 27.70% 71.60% 0.13% 0.13% GCTCTAAGC: 0.38%
Temperate Japonica  767 93.70% 3.30% 0.00% 0.00% GCTCTAAGC: 3.00%
Tropical Japonica  504 94.60% 1.00% 0.00% 0.00% GCTCTAAGC: 4.37%
Japonica Intermediate  241 64.30% 2.10% 0.00% 0.00% GCTCTAAGC: 33.61%
VI/Aromatic  96 50.00% 12.50% 0.00% 0.00% GCTCTAAGC: 37.50%
Intermediate  90 66.70% 30.00% 0.00% 0.00% GCTCTAAGC: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0501460647 G -> DEL N N silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 N N N N
vg0501460647 G -> A LOC_Os05g03460.1 upstream_gene_variant ; 715.0bp to feature; MODIFIER silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 N N N N
vg0501460647 G -> A LOC_Os05g03450.1 downstream_gene_variant ; 3327.0bp to feature; MODIFIER silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 N N N N
vg0501460647 G -> A LOC_Os05g03450-LOC_Os05g03460 intergenic_region ; MODIFIER silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 N N N N
vg0501460647 G -> GCTCTAAGC LOC_Os05g03460.1 upstream_gene_variant ; 714.0bp to feature; MODIFIER silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 N N N N
vg0501460647 G -> GCTCTAAGC LOC_Os05g03450.1 downstream_gene_variant ; 3328.0bp to feature; MODIFIER silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 N N N N
vg0501460647 G -> GCTCTAAGC LOC_Os05g03450-LOC_Os05g03460 intergenic_region ; MODIFIER silent_mutation Average:69.399; most accessible tissue: Zhenshan97 young leaf, score: 95.787 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)
vg0501460647 G A 0.05 0.0 -0.02 -0.01 0.03 0.05
vg0501460647 G GCTCT* 0.1 0.22 0.22 0.02 0.03 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501460647 NA 1.08E-14 mr1032 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
vg0501460647 NA 7.29E-16 mr1165 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
vg0501460647 NA 4.07E-15 mr1478 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
vg0501460647 NA 2.71E-08 mr1660 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
vg0501460647 NA 1.93E-08 mr1679 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
vg0501460647 NA 1.49E-06 mr1691 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
vg0501460647 NA 2.87E-07 mr1693 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
vg0501460647 NA 3.87E-07 mr1720 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
vg0501460647 NA 1.81E-06 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
vg0501460647 NA 5.81E-06 mr1755 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
vg0501460647 NA 3.70E-06 mr1772 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
vg0501460647 NA 9.22E-07 mr1321_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
vg0501460647 NA 9.40E-06 mr1355_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
vg0501460647 NA 1.52E-09 mr1598_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
vg0501460647 NA 9.73E-07 mr1679_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
vg0501460647 NA 2.93E-10 mr1756_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
vg0501460647 NA 1.46E-07 mr1895_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
vg0501460647 NA 1.88E-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
vg0501460647 NA 4.31E-11 mr1946_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
vg0501460647 NA 4.31E-11 mr1948_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
vg0501460647 NA 1.89E-07 mr1977_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