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Detailed information for vg0223043250:

Variant ID: vg0223043250 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23043250
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GTCGGCGCCGGCGGCACTAGGGGTTGCGGCAGCCCAGGACGGCGGTGGCTCCCGTCGGTGCCGGTGGCCCTAGAGGCTGCGGCGGAGGACGGCGGCAGCT[T/C]
CCGTTGGCGTTGGTGGCCCTAGGGGCGGTGGTGGCTCTCGTCGGCGCCGGCAACCCTAGGGGCTACGGTGGCCCAGGACGGCGGCGGCTCTAGGGGTTGC

Reverse complement sequence

GCAACCCCTAGAGCCGCCGCCGTCCTGGGCCACCGTAGCCCCTAGGGTTGCCGGCGCCGACGAGAGCCACCACCGCCCCTAGGGCCACCAACGCCAACGG[A/G]
AGCTGCCGCCGTCCTCCGCCGCAGCCTCTAGGGCCACCGGCACCGACGGGAGCCACCGCCGTCCTGGGCTGCCGCAACCCCTAGTGCCGCCGGCGCCGAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.40% 29.40% 0.25% 0.00% NA
All Indica  2759 90.00% 9.80% 0.22% 0.00% NA
All Japonica  1512 28.40% 71.20% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.40% 16.50% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 87.60% 12.30% 0.11% 0.00% NA
Indica Intermediate  786 92.00% 7.50% 0.51% 0.00% NA
Temperate Japonica  767 4.80% 94.70% 0.52% 0.00% NA
Tropical Japonica  504 62.50% 37.30% 0.20% 0.00% NA
Japonica Intermediate  241 32.00% 67.60% 0.41% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0223043250 T -> C LOC_Os02g38110.1 upstream_gene_variant ; 4949.0bp to feature; MODIFIER silent_mutation Average:82.737; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg0223043250 T -> C LOC_Os02g38120.1 upstream_gene_variant ; 1300.0bp to feature; MODIFIER silent_mutation Average:82.737; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg0223043250 T -> C LOC_Os02g38110-LOC_Os02g38120 intergenic_region ; MODIFIER silent_mutation Average:82.737; most accessible tissue: Zhenshan97 panicle, score: 92.533 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)
vg0223043250 T C 0.09 0.07 0.07 0.03 0.08 0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223043250 2.50E-06 NA mr1067_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
vg0223043250 9.29E-06 NA mr1072_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
vg0223043250 2.68E-06 NA mr1075_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