Search for Variation information by Variation ID:

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

Detailed information for vg0611127459:

Variant ID: vg0611127459 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11127459
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTGGCGAGGCCGGCCCGTGGTCAGGAGCACGTGCACCAGGACCCGGGCGTGGGGAGGGTGGCCCTCCAGCAGGGGCACCCTGTCCGTGGGCTGCAGCT[G/A]
GCCCAACACCTTGTCCAGGTGCATCATCCTGGAAGGACAAGTCCATGTCTAGTGAAGAAGACTTCGATGGTGCTGCAGCAGTAGAGAAAGGAAAAATCGT

Reverse complement sequence

ACGATTTTTCCTTTCTCTACTGCTGCAGCACCATCGAAGTCTTCTTCACTAGACATGGACTTGTCCTTCCAGGATGATGCACCTGGACAAGGTGTTGGGC[C/T]
AGCTGCAGCCCACGGACAGGGTGCCCCTGCTGGAGGGCCACCCTCCCCACGCCCGGGTCCTGGTGCACGTGCTCCTGACCACGGGCCGGCCTCGCCACCA

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 75.70% 19.60% 0.72% 3.94% NA
All Indica  2759 62.10% 30.00% 1.16% 6.67% NA
All Japonica  1512 94.60% 5.20% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 31.60% 63.00% 1.01% 4.37% NA
Indica II  465 90.80% 8.80% 0.00% 0.43% NA
Indica III  913 64.40% 19.50% 2.19% 13.91% NA
Indica Intermediate  786 65.60% 29.90% 0.76% 3.69% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 89.10% 10.50% 0.40% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611127459 G -> A LOC_Os06g19540.1 upstream_gene_variant ; 3786.0bp to feature; MODIFIER silent_mutation Average:83.695; most accessible tissue: Minghui63 panicle, score: 89.949 N N N N
vg0611127459 G -> A LOC_Os06g19540-LOC_Os06g19550 intergenic_region ; MODIFIER silent_mutation Average:83.695; most accessible tissue: Minghui63 panicle, score: 89.949 N N N N
vg0611127459 G -> DEL N N silent_mutation Average:83.695; most accessible tissue: Minghui63 panicle, score: 89.949 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)
vg0611127459 G A -0.02 -0.01 -0.01 -0.05 -0.06 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611127459 NA 7.77E-06 mr1857 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
vg0611127459 NA 2.36E-08 mr1857 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
vg0611127459 NA 5.19E-08 mr1860 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
vg0611127459 NA 6.41E-06 mr1931_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