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Detailed information for vg0820148135:

Variant ID: vg0820148135 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20148135
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.07, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTTTATGTATTGCACTTGTTCCCTTGAGAGGCAGAGAAAAGAAGAACAAACTCAGGGATCCTTTGGAACACAATGATTCTACGAAAATTTCATACAAC[T/C]
ATTCCAATTTTCTGCAAGAATGCAGCAAATTTCTCAATTCCAAAGGAACCTCTAAGCACCAAAGTGGAGGTTTTCTAGTCATTTTTCTACACATTGTTCA

Reverse complement sequence

TGAACAATGTGTAGAAAAATGACTAGAAAACCTCCACTTTGGTGCTTAGAGGTTCCTTTGGAATTGAGAAATTTGCTGCATTCTTGCAGAAAATTGGAAT[A/G]
GTTGTATGAAATTTTCGTAGAATCATTGTGTTCCAAAGGATCCCTGAGTTTGTTCTTCTTTTCTCTGCCTCTCAAGGGAACAAGTGCAATACATAAAAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.30% 0.04% 0.00% NA
All Indica  2759 91.40% 8.50% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 88.20% 11.40% 0.43% 0.00% NA
Indica III  913 87.70% 12.30% 0.00% 0.00% NA
Indica Intermediate  786 91.10% 8.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0820148135 T -> C LOC_Os08g32530.1 upstream_gene_variant ; 3169.0bp to feature; MODIFIER silent_mutation Average:54.89; most accessible tissue: Zhenshan97 root, score: 86.362 N N N N
vg0820148135 T -> C LOC_Os08g32520.1 downstream_gene_variant ; 2588.0bp to feature; MODIFIER silent_mutation Average:54.89; most accessible tissue: Zhenshan97 root, score: 86.362 N N N N
vg0820148135 T -> C LOC_Os08g32520-LOC_Os08g32530 intergenic_region ; MODIFIER silent_mutation Average:54.89; most accessible tissue: Zhenshan97 root, score: 86.362 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)
vg0820148135 T C -0.04 -0.03 0.0 0.0 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820148135 NA 1.53E-08 mr1301 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
vg0820148135 NA 6.87E-09 mr1410 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
vg0820148135 NA 8.93E-08 mr1093_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
vg0820148135 NA 4.23E-08 mr1235_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
vg0820148135 NA 8.14E-06 mr1403_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
vg0820148135 NA 1.66E-14 mr1410_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
vg0820148135 NA 3.40E-07 mr1622_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
vg0820148135 NA 1.21E-10 mr1993_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