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Detailed information for vg0419961351:

Variant ID: vg0419961351 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19961351
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TATGACATAAATATAGTAATTACTCCCTCCACTCCATTTCATAATATAAGTCACAACCTCTTTTTACATATTTCATAATATAAGTCATGCATGCATGTGG[A/G]
CAATTAACTATTACCCATTCTCCATTAAATTATTACTTTTTTTAAATACTCTACTCTCATGTTCTCTAATTCTATTGGATGCATGTATTGTATTTATTAG

Reverse complement sequence

CTAATAAATACAATACATGCATCCAATAGAATTAGAGAACATGAGAGTAGAGTATTTAAAAAAAGTAATAATTTAATGGAGAATGGGTAATAGTTAATTG[T/C]
CCACATGCATGCATGACTTATATTATGAAATATGTAAAAAGAGGTTGTGACTTATATTATGAAATGGAGTGGAGGGAGTAATTACTATATTTATGTCATA

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 72.00% 27.70% 0.28% 0.00% NA
All Indica  2759 84.50% 15.30% 0.22% 0.00% NA
All Japonica  1512 45.40% 54.40% 0.20% 0.00% NA
Aus  269 92.60% 7.10% 0.37% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 86.70% 13.30% 0.00% 0.00% NA
Indica III  913 73.50% 26.20% 0.33% 0.00% NA
Indica Intermediate  786 85.40% 14.20% 0.38% 0.00% NA
Temperate Japonica  767 22.40% 77.40% 0.13% 0.00% NA
Tropical Japonica  504 85.10% 14.70% 0.20% 0.00% NA
Japonica Intermediate  241 35.30% 64.30% 0.41% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 65.60% 31.10% 3.33% 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
vg0419961351 A -> G LOC_Os04g32980-LOC_Os04g33010 intergenic_region ; MODIFIER silent_mutation Average:82.418; most accessible tissue: Minghui63 flower, score: 96.791 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)
vg0419961351 A G -0.03 -0.01 0.0 0.03 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419961351 2.08E-06 1.45E-08 mr1080_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
vg0419961351 3.72E-07 1.68E-08 mr1619_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
vg0419961351 NA 5.51E-06 mr1888_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