Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0427996435:

Variant ID: vg0427996435 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27996435
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.52, A: 0.47, T: 0.01, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATTACGGAATAGAATGTAGTAGTTTTCTTAAAAAGAAAATTCAATTAATATCCAGTAACCAGTTTGATCTGCTACTCCCTCCGTCCCAAAAAATAAG[A/G]
CATATCCATCCAAAATTACTTATATTTTGGGGCGGAGACATCATAAGATTTGTTCTATGGATTGTTAGGCTGTGTTCCTCTCTACACTTTCATATCCTCT

Reverse complement sequence

AGAGGATATGAAAGTGTAGAGAGGAACACAGCCTAACAATCCATAGAACAAATCTTATGATGTCTCCGCCCCAAAATATAAGTAATTTTGGATGGATATG[T/C]
CTTATTTTTTGGGACGGAGGGAGTAGCAGATCAAACTGGTTACTGGATATTAATTGAATTTTCTTTTTAAGAAAACTACTACATTCTATTCCGTAATAAT

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 57.80% 41.50% 0.38% 0.25% NA
All Indica  2759 91.50% 7.80% 0.54% 0.18% NA
All Japonica  1512 0.80% 98.70% 0.00% 0.46% NA
Aus  269 59.10% 40.50% 0.37% 0.00% NA
Indica I  595 94.60% 4.40% 0.84% 0.17% NA
Indica II  465 94.60% 4.30% 0.65% 0.43% NA
Indica III  913 87.30% 12.40% 0.22% 0.11% NA
Indica Intermediate  786 92.10% 7.10% 0.64% 0.13% NA
Temperate Japonica  767 0.50% 98.60% 0.00% 0.91% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 41.10% 56.70% 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
vg0427996435 A -> DEL N N silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 N N N N
vg0427996435 A -> G LOC_Os04g47130.1 upstream_gene_variant ; 4048.0bp to feature; MODIFIER silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 N N N N
vg0427996435 A -> G LOC_Os04g47140.1 upstream_gene_variant ; 615.0bp to feature; MODIFIER silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 N N N N
vg0427996435 A -> G LOC_Os04g47150.1 upstream_gene_variant ; 706.0bp to feature; MODIFIER silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 N N N N
vg0427996435 A -> G LOC_Os04g47140.3 upstream_gene_variant ; 603.0bp to feature; MODIFIER silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 N N N N
vg0427996435 A -> G LOC_Os04g47140.2 upstream_gene_variant ; 603.0bp to feature; MODIFIER silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 N N N N
vg0427996435 A -> G LOC_Os04g47140-LOC_Os04g47150 intergenic_region ; MODIFIER silent_mutation Average:65.889; most accessible tissue: Minghui63 young leaf, score: 82.087 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)
vg0427996435 A G -0.01 -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
vg0427996435 NA 1.63E-09 mr1663 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
vg0427996435 NA 2.30E-06 mr1134_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
vg0427996435 NA 2.75E-06 mr1137_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
vg0427996435 NA 4.86E-37 mr1181_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
vg0427996435 NA 8.43E-06 mr1181_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
vg0427996435 NA 7.65E-06 mr1329_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
vg0427996435 3.71E-06 3.71E-06 mr1367_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
vg0427996435 NA 6.34E-06 mr1745_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