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Detailed information for vg0726784828:

Variant ID: vg0726784828 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26784828
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


AAACTGTAATAAGAGTGCCAAAGTACTGAAAGAGAAGTGCAGATGACTCAAGAGTTGCAAATTTCTGCCATATGTAAAAGCTTCTGTTCTTTATTGTGTA[G/A]
ATATATTTTGACCCTTGAATATTTGAACATTGGTAATGGTAATATGATGTAATCCTAGTTGGCCAAAATCATGTCCAATTAGCTCAAATTCTCTGTCCAT

Reverse complement sequence

ATGGACAGAGAATTTGAGCTAATTGGACATGATTTTGGCCAACTAGGATTACATCATATTACCATTACCAATGTTCAAATATTCAAGGGTCAAAATATAT[C/T]
TACACAATAAAGAACAGAAGCTTTTACATATGGCAGAAATTTGCAACTCTTGAGTCATCTGCACTTCTCTTTCAGTACTTTGGCACTCTTATTACAGTTT

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 37.80% 27.10% 10.22% 24.88% NA
All Indica  2759 5.60% 41.60% 15.11% 37.66% NA
All Japonica  1512 98.30% 0.90% 0.07% 0.66% NA
Aus  269 35.70% 20.40% 17.10% 26.77% NA
Indica I  595 11.80% 15.30% 33.11% 39.83% NA
Indica II  465 3.70% 42.80% 14.19% 39.35% NA
Indica III  913 1.20% 60.60% 8.32% 29.90% NA
Indica Intermediate  786 7.30% 38.80% 9.92% 44.02% NA
Temperate Japonica  767 99.00% 0.00% 0.00% 1.04% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 1.70% 0.41% 0.83% NA
VI/Aromatic  96 2.10% 43.80% 11.46% 42.71% NA
Intermediate  90 50.00% 25.60% 8.89% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0726784828 G -> DEL N N silent_mutation Average:81.36; most accessible tissue: Zhenshan97 root, score: 92.789 N N N N
vg0726784828 G -> A LOC_Os07g44860.1 upstream_gene_variant ; 265.0bp to feature; MODIFIER silent_mutation Average:81.36; most accessible tissue: Zhenshan97 root, score: 92.789 N N N N
vg0726784828 G -> A LOC_Os07g44850.1 downstream_gene_variant ; 3321.0bp to feature; MODIFIER silent_mutation Average:81.36; most accessible tissue: Zhenshan97 root, score: 92.789 N N N N
vg0726784828 G -> A LOC_Os07g44870.1 downstream_gene_variant ; 169.0bp to feature; MODIFIER silent_mutation Average:81.36; most accessible tissue: Zhenshan97 root, score: 92.789 N N N N
vg0726784828 G -> A LOC_Os07g44880.1 downstream_gene_variant ; 2032.0bp to feature; MODIFIER silent_mutation Average:81.36; most accessible tissue: Zhenshan97 root, score: 92.789 N N N N
vg0726784828 G -> A LOC_Os07g44860-LOC_Os07g44870 intergenic_region ; MODIFIER silent_mutation Average:81.36; most accessible tissue: Zhenshan97 root, score: 92.789 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)
vg0726784828 G A -0.1 0.01 -0.01 -0.01 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726784828 NA 6.95E-10 mr1336 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
vg0726784828 NA 6.12E-11 mr1751 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
vg0726784828 NA 7.01E-07 mr1915 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
vg0726784828 NA 1.47E-06 mr1128_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
vg0726784828 NA 3.54E-06 mr1152_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
vg0726784828 NA 1.21E-26 mr1323_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
vg0726784828 NA 1.29E-10 mr1646_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
vg0726784828 NA 6.96E-06 mr1646_2 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
vg0726784828 NA 2.11E-10 mr1806_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