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Detailed information for vg0204707409:

Variant ID: vg0204707409 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4707409
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCGTCCCAAAATAAGTGTAGTTTTACACTATTCACGTTCAACGTTTGACCGTTCGTCTTATTTGAATTTTTTTTATAATTAGTATTTTTATTGCTATTA[G/A]
ATGATAAAACATGAATAATACTTTATGTGTGACTAAATATTTTCAATTTTTTCACAAATTTTTTAAATAAGATGGATGGTCAAACGTTGGGCACAGATAT

Reverse complement sequence

ATATCTGTGCCCAACGTTTGACCATCCATCTTATTTAAAAAATTTGTGAAAAAATTGAAAATATTTAGTCACACATAAAGTATTATTCATGTTTTATCAT[C/T]
TAATAGCAATAAAAATACTAATTATAAAAAAAATTCAAATAAGACGAACGGTCAAACGTTGAACGTGAATAGTGTAAAACTACACTTATTTTGGGACGGG

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 97.30% 0.40% 0.36% 1.90% NA
All Indica  2759 97.70% 0.40% 0.11% 1.81% NA
All Japonica  1512 97.40% 0.30% 0.93% 1.39% NA
Aus  269 94.10% 0.70% 0.00% 5.20% NA
Indica I  595 97.60% 0.70% 0.17% 1.51% NA
Indica II  465 95.50% 0.40% 0.00% 4.09% NA
Indica III  913 98.80% 0.40% 0.00% 0.77% NA
Indica Intermediate  786 97.80% 0.00% 0.25% 1.91% NA
Temperate Japonica  767 98.60% 0.10% 1.17% 0.13% NA
Tropical Japonica  504 95.40% 0.80% 0.79% 2.98% NA
Japonica Intermediate  241 97.50% 0.00% 0.41% 2.07% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 94.40% 2.20% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204707409 G -> A LOC_Os02g09160.1 upstream_gene_variant ; 881.0bp to feature; MODIFIER silent_mutation Average:77.431; most accessible tissue: Minghui63 young leaf, score: 91.428 N N N N
vg0204707409 G -> A LOC_Os02g09170.1 upstream_gene_variant ; 1084.0bp to feature; MODIFIER silent_mutation Average:77.431; most accessible tissue: Minghui63 young leaf, score: 91.428 N N N N
vg0204707409 G -> A LOC_Os02g09170.2 upstream_gene_variant ; 1084.0bp to feature; MODIFIER silent_mutation Average:77.431; most accessible tissue: Minghui63 young leaf, score: 91.428 N N N N
vg0204707409 G -> A LOC_Os02g09160-LOC_Os02g09170 intergenic_region ; MODIFIER silent_mutation Average:77.431; most accessible tissue: Minghui63 young leaf, score: 91.428 N N N N
vg0204707409 G -> DEL N N silent_mutation Average:77.431; most accessible tissue: Minghui63 young leaf, score: 91.428 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)
vg0204707409 G A -0.02 -0.01 -0.01 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204707409 1.77E-07 1.77E-07 mr1926 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