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Detailed information for vg0921543752:

Variant ID: vg0921543752 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21543752
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, T: 0.14, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


ACCATCCAACCAACGATAAACCAATTGAAACAAGCTGCTGCGAGGACAGGACCAAATGAGCTTCGCCTCACCACGATGAAGACATGCGACCGAGCAACAA[A/T]
CTTAAAGATTAGAGTAAGTCTATTATTCACCTCTCGAGATGGCGTCCAATCGTTTTTCATATAGTTTGAAAGATTATCAAAAACTTAAAAAAAATAAACA

Reverse complement sequence

TGTTTATTTTTTTTAAGTTTTTGATAATCTTTCAAACTATATGAAAAACGATTGGACGCCATCTCGAGAGGTGAATAATAGACTTACTCTAATCTTTAAG[T/A]
TTGTTGCTCGGTCGCATGTCTTCATCGTGGTGAGGCGAAGCTCATTTGGTCCTGTCCTCGCAGCAGCTTGTTTCAATTGGTTTATCGTTGGTTGGATGGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.60% 19.10% 0.30% 0.00% NA
All Indica  2759 67.70% 31.90% 0.47% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 85.70% 13.80% 0.50% 0.00% NA
Indica II  465 65.40% 33.30% 1.29% 0.00% NA
Indica III  913 59.30% 40.60% 0.11% 0.00% NA
Indica Intermediate  786 65.10% 34.50% 0.38% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 10.00% 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
vg0921543752 A -> T LOC_Os09g37280.1 upstream_gene_variant ; 803.0bp to feature; MODIFIER silent_mutation Average:72.311; most accessible tissue: Callus, score: 95.858 N N N N
vg0921543752 A -> T LOC_Os09g37280.2 upstream_gene_variant ; 803.0bp to feature; MODIFIER silent_mutation Average:72.311; most accessible tissue: Callus, score: 95.858 N N N N
vg0921543752 A -> T LOC_Os09g37290.1 downstream_gene_variant ; 122.0bp to feature; MODIFIER silent_mutation Average:72.311; most accessible tissue: Callus, score: 95.858 N N N N
vg0921543752 A -> T LOC_Os09g37300.1 downstream_gene_variant ; 596.0bp to feature; MODIFIER silent_mutation Average:72.311; most accessible tissue: Callus, score: 95.858 N N N N
vg0921543752 A -> T LOC_Os09g37280-LOC_Os09g37290 intergenic_region ; MODIFIER silent_mutation Average:72.311; most accessible tissue: Callus, score: 95.858 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)
vg0921543752 A T 0.01 0.03 0.0 0.0 -0.01 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921543752 3.72E-10 NA mr1003 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
vg0921543752 8.36E-09 3.32E-09 mr1003 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
vg0921543752 7.29E-06 6.21E-09 mr1004 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
vg0921543752 NA 1.91E-08 mr1004 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
vg0921543752 1.86E-08 6.61E-13 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
vg0921543752 3.75E-07 9.61E-13 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
vg0921543752 1.05E-07 1.06E-12 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
vg0921543752 1.27E-06 3.79E-12 mr1007 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
vg0921543752 NA 5.58E-06 mr1037 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
vg0921543752 5.20E-10 NA mr1051 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
vg0921543752 4.68E-09 2.52E-10 mr1051 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
vg0921543752 1.49E-08 1.79E-13 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
vg0921543752 2.20E-07 2.13E-13 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
vg0921543752 1.29E-08 NA mr1536 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
vg0921543752 2.20E-09 2.39E-12 mr1536 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
vg0921543752 2.87E-10 4.65E-16 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
vg0921543752 3.58E-08 3.43E-11 mr1004_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
vg0921543752 1.31E-10 1.08E-14 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
vg0921543752 8.51E-09 5.09E-14 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
vg0921543752 2.93E-13 NA mr1051_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
vg0921543752 2.83E-11 1.58E-13 mr1051_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
vg0921543752 1.18E-09 NA mr1536_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
vg0921543752 7.57E-10 2.21E-13 mr1536_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
vg0921543752 4.24E-06 1.90E-11 mr1986_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
vg0921543752 NA 6.58E-07 mr1986_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