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Detailed information for vg0221905933:

Variant ID: vg0221905933 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21905933
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: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CGGAGAAGCCGTTCGCGCGGAAGGCGTCCGGGACCGGCCGCGCGGCGAGCCGCTGGTCGTGCTTCGTGTAGGCCTCCCTCGCGGCCTCGGCCGACGACAC[G/A]
ACCACGGCCGTGGTGAGGCCTAGCTTCAGCGTCATGACAGGGCCATGGACGCGCGCCAGTTTCGCGAGGGTTTGGTGGAAGATGCCGCCAAGGCAGAGTA

Reverse complement sequence

TACTCTGCCTTGGCGGCATCTTCCACCAAACCCTCGCGAAACTGGCGCGCGTCCATGGCCCTGTCATGACGCTGAAGCTAGGCCTCACCACGGCCGTGGT[C/T]
GTGTCGTCGGCCGAGGCCGCGAGGGAGGCCTACACGAAGCACGACCAGCGGCTCGCCGCGCGGCCGGTCCCGGACGCCTTCCGCGCGAACGGCTTCTCCG

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 96.50% 2.70% 0.85% 0.00% NA
All Indica  2759 94.20% 4.50% 1.30% 0.00% NA
All Japonica  1512 99.70% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 74.40% 20.20% 5.38% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 95.00% 3.70% 1.27% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0221905933 G -> A LOC_Os02g36280.1 synonymous_variant ; p.Val115Val; LOW synonymous_codon Average:80.341; most accessible tissue: Callus, score: 94.531 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)
vg0221905933 G A -0.08 -0.03 -0.03 -0.02 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221905933 NA 5.42E-07 mr1044 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
vg0221905933 NA 2.44E-06 mr1069 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
vg0221905933 NA 2.89E-06 mr1075 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
vg0221905933 NA 1.71E-07 mr1076 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
vg0221905933 5.03E-07 4.31E-10 mr1077 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
vg0221905933 NA 5.25E-07 mr1082 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
vg0221905933 NA 3.93E-07 mr1441 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
vg0221905933 NA 7.67E-07 mr1560 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