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Detailed information for vg0325617211:

Variant ID: vg0325617211 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 25617211
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTAAAAAAATTAAAAACATAAGTCACAAGTAAAGTACTATTCATGTTTTATCATCTCATAGCAACAAAAATGCTAATTATAAAAAAATTTTAAATAA[A/G]
ACGGACAGTCAAAGTTGGACGCGGAAAACCATGGCTGCACTTATTTTAAGACGGAGGTAGTATTTAGTACAAGTAATATAGAAATGCCGTCATTGATCCT

Reverse complement sequence

AGGATCAATGACGGCATTTCTATATTACTTGTACTAAATACTACCTCCGTCTTAAAATAAGTGCAGCCATGGTTTTCCGCGTCCAACTTTGACTGTCCGT[T/C]
TTATTTAAAATTTTTTTATAATTAGCATTTTTGTTGCTATGAGATGATAAAACATGAATAGTACTTTACTTGTGACTTATGTTTTTAATTTTTTTAAAAA

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 87.50% 12.40% 0.04% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 67.80% 32.10% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 71.60% 28.40% 0.00% 0.00% NA
Tropical Japonica  504 71.60% 28.20% 0.20% 0.00% NA
Japonica Intermediate  241 47.70% 51.90% 0.41% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0325617211 A -> G LOC_Os03g45370.1 downstream_gene_variant ; 997.0bp to feature; MODIFIER silent_mutation Average:90.176; most accessible tissue: Minghui63 root, score: 98.797 N N N N
vg0325617211 A -> G LOC_Os03g45370-LOC_Os03g45390 intergenic_region ; MODIFIER silent_mutation Average:90.176; most accessible tissue: Minghui63 root, score: 98.797 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)
vg0325617211 A G 0.02 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325617211 NA 4.61E-07 mr1209 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
vg0325617211 2.96E-08 2.95E-08 mr1597 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
vg0325617211 3.16E-06 3.16E-06 mr1597 Jap_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
vg0325617211 NA 1.30E-06 mr1979 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
vg0325617211 6.68E-06 NA mr1745_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