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Detailed information for vg0805055129:

Variant ID: vg0805055129 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5055129
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, C: 0.40, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTTACTTAAGATGGTTTTTGACGCAAGGGAATTATACCACTAGCTATAAATAATTTTAGAATGGTGCTTTCGTTCGGTTAATTAAAGAGGTTTGGCGC[G/C]
CGTCATGAATTATTGATCAGTCTACTGAAATACTCCCTCCGTTTCAAAATATTTGACGCCGTTGACTTTTTTAAATATGTTTGACCGTTCGTCTTATTTA

Reverse complement sequence

TAAATAAGACGAACGGTCAAACATATTTAAAAAAGTCAACGGCGTCAAATATTTTGAAACGGAGGGAGTATTTCAGTAGACTGATCAATAATTCATGACG[C/G]
GCGCCAAACCTCTTTAATTAACCGAACGAAAGCACCATTCTAAAATTATTTATAGCTAGTGGTATAATTCCCTTGCGTCAAAAACCATCTTAAGTAACAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.90% 29.00% 0.28% 33.83% NA
All Indica  2759 52.50% 4.50% 0.33% 42.70% NA
All Japonica  1512 11.00% 77.90% 0.20% 10.85% NA
Aus  269 29.00% 11.90% 0.37% 58.74% NA
Indica I  595 89.90% 2.40% 0.17% 7.56% NA
Indica II  465 24.50% 8.00% 0.65% 66.88% NA
Indica III  913 41.90% 3.00% 0.00% 55.09% NA
Indica Intermediate  786 52.90% 5.90% 0.64% 40.59% NA
Temperate Japonica  767 2.00% 89.60% 0.39% 8.08% NA
Tropical Japonica  504 20.60% 67.90% 0.00% 11.51% NA
Japonica Intermediate  241 19.90% 61.80% 0.00% 18.26% NA
VI/Aromatic  96 20.80% 11.50% 0.00% 67.71% NA
Intermediate  90 33.30% 28.90% 0.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805055129 G -> C LOC_Os08g08720.1 downstream_gene_variant ; 892.0bp to feature; MODIFIER silent_mutation Average:26.877; most accessible tissue: Zhenshan97 root, score: 87.09 N N N N
vg0805055129 G -> C LOC_Os08g08730.1 downstream_gene_variant ; 3823.0bp to feature; MODIFIER silent_mutation Average:26.877; most accessible tissue: Zhenshan97 root, score: 87.09 N N N N
vg0805055129 G -> C LOC_Os08g08720-LOC_Os08g08730 intergenic_region ; MODIFIER silent_mutation Average:26.877; most accessible tissue: Zhenshan97 root, score: 87.09 N N N N
vg0805055129 G -> DEL N N silent_mutation Average:26.877; most accessible tissue: Zhenshan97 root, score: 87.09 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)
vg0805055129 G C -0.11 -0.02 -0.02 -0.01 -0.03 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805055129 NA 8.98E-08 mr1082 Jap_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
vg0805055129 NA 3.89E-06 mr1082_2 Jap_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
vg0805055129 3.73E-06 3.73E-06 mr1440_2 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
vg0805055129 NA 5.70E-08 mr1896_2 Jap_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