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Detailed information for vg0805761726:

Variant ID: vg0805761726 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5761726
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TCGATCTTAGATGCCTATCGATCTGGAGCGGAGAGACGACCCATGGCATTGACCGAACGACAAACATCGGCGGCGGTGTGTAGGCAACGACGGGACGGTG[G/A]
GGAGGCCAGGTACAGCGGGAGGCGCGGCTGCGGTGGTGGGCGTGTTGGCCAACAGGTGGGCGGCATAGCACGTGCCACGTACTGCTGCTGGCAGCAAGCA

Reverse complement sequence

TGCTTGCTGCCAGCAGCAGTACGTGGCACGTGCTATGCCGCCCACCTGTTGGCCAACACGCCCACCACCGCAGCCGCGCCTCCCGCTGTACCTGGCCTCC[C/T]
CACCGTCCCGTCGTTGCCTACACACCGCCGCCGATGTTTGTCGTTCGGTCAATGCCATGGGTCGTCTCTCCGCTCCAGATCGATAGGCATCTAAGATCGA

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 54.10% 45.90% 0.00% 0.00% NA
All Indica  2759 31.40% 68.60% 0.00% 0.00% NA
All Japonica  1512 98.30% 1.70% 0.00% 0.00% NA
Aus  269 28.60% 71.40% 0.00% 0.00% NA
Indica I  595 5.20% 94.80% 0.00% 0.00% NA
Indica II  465 44.30% 55.70% 0.00% 0.00% NA
Indica III  913 42.10% 57.90% 0.00% 0.00% NA
Indica Intermediate  786 31.00% 69.00% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0805761726 G -> A LOC_Os08g09970.1 missense_variant ; p.Gly20Glu; MODERATE nonsynonymous_codon ; G20E Average:72.151; most accessible tissue: Zhenshan97 panicle, score: 89.143 unknown unknown TOLERATED 1.00

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)
vg0805761726 G A -0.05 -0.03 -0.03 -0.06 -0.07 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805761726 2.60E-06 NA mr1177 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
vg0805761726 NA 9.49E-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
vg0805761726 NA 5.48E-14 mr1807 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
vg0805761726 NA 3.54E-06 mr1807 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
vg0805761726 NA 1.18E-08 mr1986 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