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Detailed information for vg0804308209:

Variant ID: vg0804308209 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4308209
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, G: 0.26, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCCCGCCCACCCAACACCACACCTCACATGTGTGGCACACCTGCTTTCTTCAGCATGCACACCTCCTCCACTGACACTAGAGAGCGCCACAACTGTTG[A/G]
TGCTATGCCAAAAATGGTTGTAATGGCAACTCTCCCTCCTCTTGCCCCCTCCACCTCTACTTCCCTACCATTCTCTTCCCTGCCTTTTCTTCCCCAACTA

Reverse complement sequence

TAGTTGGGGAAGAAAAGGCAGGGAAGAGAATGGTAGGGAAGTAGAGGTGGAGGGGGCAAGAGGAGGGAGAGTTGCCATTACAACCATTTTTGGCATAGCA[T/C]
CAACAGTTGTGGCGCTCTCTAGTGTCAGTGGAGGAGGTGTGCATGCTGAAGAAAGCAGGTGTGCCACACATGTGAGGTGTGGTGTTGGGTGGGCGGGGAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.10% 21.60% 0.08% 0.28% NA
All Indica  2759 89.30% 10.30% 0.00% 0.40% NA
All Japonica  1512 52.40% 47.20% 0.26% 0.13% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 91.00% 8.40% 0.00% 0.65% NA
Indica III  913 83.00% 16.30% 0.00% 0.66% NA
Indica Intermediate  786 87.80% 12.00% 0.00% 0.25% NA
Temperate Japonica  767 57.00% 42.50% 0.52% 0.00% NA
Tropical Japonica  504 60.10% 39.70% 0.00% 0.20% NA
Japonica Intermediate  241 22.00% 77.60% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0804308209 A -> G LOC_Os08g07700.1 upstream_gene_variant ; 3513.0bp to feature; MODIFIER silent_mutation Average:69.675; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0804308209 A -> G LOC_Os08g07710.1 upstream_gene_variant ; 3575.0bp to feature; MODIFIER silent_mutation Average:69.675; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0804308209 A -> G LOC_Os08g07700-LOC_Os08g07710 intergenic_region ; MODIFIER silent_mutation Average:69.675; most accessible tissue: Zhenshan97 flower, score: 93.655 N N N N
vg0804308209 A -> DEL N N silent_mutation Average:69.675; most accessible tissue: Zhenshan97 flower, score: 93.655 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)
vg0804308209 A G 0.0 0.01 0.0 0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804308209 7.39E-11 1.78E-09 mr1174 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
vg0804308209 5.34E-13 2.41E-15 mr1174 Jap_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
vg0804308209 4.64E-08 4.64E-08 mr1347 Jap_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
vg0804308209 7.45E-13 NA mr1174_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
vg0804308209 5.55E-12 2.06E-12 mr1174_2 Jap_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
vg0804308209 8.96E-08 NA mr1347_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
vg0804308209 8.37E-08 NA mr1347_2 Jap_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