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Detailed information for vg0819041897:

Variant ID: vg0819041897 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19041897
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGAAAATCAAGTTTTTACATATGGTTGTGGAGCCGTATATATAAATCCTACTAATTTTTACCAACATCTAGTTTCGGGTGGATGCCCTAACCATTTAT[G/A]
AAAAGAAATTCGCGCACGGATGCTCTACCACCCGTATGGACCCTTGGTATGTGGCGGAGCTTATGACTGCCAACAATAACCTATTTTGGTTGCTACAAAA

Reverse complement sequence

TTTTGTAGCAACCAAAATAGGTTATTGTTGGCAGTCATAAGCTCCGCCACATACCAAGGGTCCATACGGGTGGTAGAGCATCCGTGCGCGAATTTCTTTT[C/T]
ATAAATGGTTAGGGCATCCACCCGAAACTAGATGTTGGTAAAAATTAGTAGGATTTATATATACGGCTCCACAACCATATGTAAAAACTTGATTTTCTTC

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 92.40% 7.60% 0.00% 0.00% NA
All Indica  2759 87.20% 12.80% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 74.40% 25.60% 0.00% 0.00% NA
Indica Intermediate  786 89.90% 10.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0819041897 G -> A LOC_Os08g30840.1 upstream_gene_variant ; 3451.0bp to feature; MODIFIER silent_mutation Average:66.087; most accessible tissue: Zhenshan97 flower, score: 96.309 N N N N
vg0819041897 G -> A LOC_Os08g30850.1 upstream_gene_variant ; 1853.0bp to feature; MODIFIER silent_mutation Average:66.087; most accessible tissue: Zhenshan97 flower, score: 96.309 N N N N
vg0819041897 G -> A LOC_Os08g30840-LOC_Os08g30850 intergenic_region ; MODIFIER silent_mutation Average:66.087; most accessible tissue: Zhenshan97 flower, score: 96.309 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)
vg0819041897 G A 0.07 0.01 -0.01 0.03 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819041897 NA 5.91E-08 Yield Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652