Search for Variation information by Variation ID:

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

Detailed information for vg0419095970:

Variant ID: vg0419095970 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19095970
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: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GTACGCCACCTTGTCGTAAACTCGACGGTATGAGGCTGTGTTTAGTTCAGCGCAAAGTTTAGATTTTGGTTGAAATTGAAGATGATGTGACTGAAAAGTT[G/A]
TGTGTATGACAGGTTGATGTGATGGAAAAGAACTGAAGTTTGTATCCAAACTTTGGATCCAGACACAGGGATTCCTCGGTGCATTCACTCTACTACTCCC

Reverse complement sequence

GGGAGTAGTAGAGTGAATGCACCGAGGAATCCCTGTGTCTGGATCCAAAGTTTGGATACAAACTTCAGTTCTTTTCCATCACATCAACCTGTCATACACA[C/T]
AACTTTTCAGTCACATCATCTTCAATTTCAACCAAAATCTAAACTTTGCGCTGAACTAAACACAGCCTCATACCGTCGAGTTTACGACAAGGTGGCGTAC

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 81.20% 18.50% 0.21% 0.06% NA
All Indica  2759 71.80% 27.70% 0.33% 0.11% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 61.00% 38.70% 0.37% 0.00% NA
Indica I  595 67.20% 32.10% 0.50% 0.17% NA
Indica II  465 90.50% 9.20% 0.00% 0.22% NA
Indica III  913 68.70% 31.00% 0.22% 0.11% NA
Indica Intermediate  786 67.90% 31.60% 0.51% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0419095970 G -> DEL N N silent_mutation Average:82.066; most accessible tissue: Zhenshan97 flower, score: 95.274 N N N N
vg0419095970 G -> A LOC_Os04g31890-LOC_Os04g31900 intergenic_region ; MODIFIER silent_mutation Average:82.066; most accessible tissue: Zhenshan97 flower, score: 95.274 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)
vg0419095970 G A -0.03 -0.04 -0.05 -0.05 -0.05 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419095970 NA 8.77E-07 mr1708 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