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Detailed information for vg0528034305:

Variant ID: vg0528034305 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28034305
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, G: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TATAAAATCTAAAAGTACATAATGAAAAATAGACTTTAATAAAAAAATTTTAAAACCAGCTATAAATTTAAGGTTAAAAATTTAAATTTTGGCTAATATA[T/G]
GTGGGCATAAGCAAAAAAGACGAGGCCCCGGGCTCCTCTGCTTCTTTTGGGCAATAGCTTCGCGTAGCTTAGCTCGGCTTCCCCCTCATTCATGGCCATT

Reverse complement sequence

AATGGCCATGAATGAGGGGGAAGCCGAGCTAAGCTACGCGAAGCTATTGCCCAAAAGAAGCAGAGGAGCCCGGGGCCTCGTCTTTTTTGCTTATGCCCAC[A/C]
TATATTAGCCAAAATTTAAATTTTTAACCTTAAATTTATAGCTGGTTTTAAAATTTTTTTATTAAAGTCTATTTTTCATTATGTACTTTTAGATTTTATA

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 59.10% 40.70% 0.23% 0.00% NA
All Indica  2759 34.90% 64.70% 0.36% 0.00% NA
All Japonica  1512 94.40% 5.60% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 4.20% 95.60% 0.17% 0.00% NA
Indica II  465 66.50% 33.50% 0.00% 0.00% NA
Indica III  913 37.60% 62.10% 0.33% 0.00% NA
Indica Intermediate  786 36.50% 62.70% 0.76% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.50% 0.41% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 0.00% 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
vg0528034305 T -> G LOC_Os05g48870.1 upstream_gene_variant ; 75.0bp to feature; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0528034305 T -> G LOC_Os05g48870.6 upstream_gene_variant ; 3704.0bp to feature; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0528034305 T -> G LOC_Os05g48870.8 upstream_gene_variant ; 3704.0bp to feature; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0528034305 T -> G LOC_Os05g48870.9 upstream_gene_variant ; 3704.0bp to feature; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0528034305 T -> G LOC_Os05g48870.5 upstream_gene_variant ; 3704.0bp to feature; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0528034305 T -> G LOC_Os05g48870.7 upstream_gene_variant ; 3704.0bp to feature; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 N N N N
vg0528034305 T -> G LOC_Os05g48860-LOC_Os05g48870 intergenic_region ; MODIFIER silent_mutation Average:96.665; most accessible tissue: Zhenshan97 panicle, score: 98.621 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)
vg0528034305 T G 0.1 0.08 0.05 0.04 0.06 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528034305 NA 1.82E-15 mr1059 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
vg0528034305 NA 3.54E-09 mr1059 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
vg0528034305 NA 1.36E-17 mr1143 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
vg0528034305 NA 4.28E-12 mr1143 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
vg0528034305 NA 2.83E-17 mr1167 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
vg0528034305 NA 2.62E-11 mr1167 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
vg0528034305 NA 1.42E-16 mr1535 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
vg0528034305 NA 4.31E-11 mr1535 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
vg0528034305 NA 2.54E-15 mr1675 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
vg0528034305 NA 4.78E-10 mr1675 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
vg0528034305 NA 6.89E-06 mr1698 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
vg0528034305 NA 1.40E-08 mr1726 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
vg0528034305 NA 8.15E-06 mr1835 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
vg0528034305 NA 2.74E-08 mr1860 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
vg0528034305 NA 8.99E-06 mr1904 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
vg0528034305 NA 1.49E-06 mr1925 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
vg0528034305 NA 5.10E-07 mr1950 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
vg0528034305 NA 3.44E-15 mr1969 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
vg0528034305 NA 2.58E-11 mr1969 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
vg0528034305 NA 1.57E-17 mr1995 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
vg0528034305 NA 3.07E-12 mr1995 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
vg0528034305 NA 1.54E-19 mr1167_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
vg0528034305 NA 6.42E-10 mr1167_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
vg0528034305 NA 1.28E-09 mr1352_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
vg0528034305 NA 6.78E-07 mr1726_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
vg0528034305 NA 1.52E-14 mr1950_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
vg0528034305 NA 2.99E-06 mr1950_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