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Detailed information for vg0223598375:

Variant ID: vg0223598375 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23598375
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.09, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GCTAAAAGCACTTGAAATCATCTAGCTCAGCGTTCACTTCCCTGTTAATGTAGACTTTATAGGTGATGAGGTGAATCAAGTAAAATGTTTGTAGCATTTC[A/G]
CCCGTTAGAGTGTATTCCTGTTGAAGAGTAGGAGATCCTTGAGATTGTTGATGTCCAATCCTTTGTATTTTGTAACTTGTTCCTGCGATACCTATTGCCG

Reverse complement sequence

CGGCAATAGGTATCGCAGGAACAAGTTACAAAATACAAAGGATTGGACATCAACAATCTCAAGGATCTCCTACTCTTCAACAGGAATACACTCTAACGGG[T/C]
GAAATGCTACAAACATTTTACTTGATTCACCTCATCACCTATAAAGTCTACATTAACAGGGAAGTGAACGCTGAGCTAGATGATTTCAAGTGCTTTTAGC

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 56.60% 42.90% 0.36% 0.13% NA
All Indica  2759 41.10% 58.20% 0.54% 0.18% NA
All Japonica  1512 80.50% 19.40% 0.00% 0.07% NA
Aus  269 69.90% 30.10% 0.00% 0.00% NA
Indica I  595 49.70% 49.20% 0.67% 0.34% NA
Indica II  465 40.60% 58.50% 0.65% 0.22% NA
Indica III  913 34.30% 65.60% 0.11% 0.00% NA
Indica Intermediate  786 42.70% 56.10% 0.89% 0.25% NA
Temperate Japonica  767 98.00% 1.80% 0.00% 0.13% NA
Tropical Japonica  504 49.20% 50.80% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 10.00% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 13.50% 1.04% 0.00% NA
Intermediate  90 62.20% 36.70% 1.11% 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
vg0223598375 A -> G LOC_Os02g39070.1 intron_variant ; MODIFIER silent_mutation Average:85.448; most accessible tissue: Zhenshan97 flag leaf, score: 92.878 N N N N
vg0223598375 A -> G LOC_Os02g39070.2 intron_variant ; MODIFIER silent_mutation Average:85.448; most accessible tissue: Zhenshan97 flag leaf, score: 92.878 N N N N
vg0223598375 A -> DEL N N silent_mutation Average:85.448; most accessible tissue: Zhenshan97 flag leaf, score: 92.878 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)
vg0223598375 A G 0.0 0.0 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223598375 NA 9.06E-07 mr1746 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
vg0223598375 9.09E-06 3.39E-09 mr1227_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
vg0223598375 NA 2.87E-06 mr1594_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
vg0223598375 1.29E-06 NA mr1746_2 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
vg0223598375 4.08E-06 1.53E-11 mr1746_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