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Detailed information for vg0208132368:

Variant ID: vg0208132368 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8132368
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.24, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:


AATGCAAAGCTGGTGAAGGCCCGTTTCTTCACTCCCCTTGGTTGGTACTTTTAGGGCATGTTTGATACAGCTCCAACTCATAAATTTAACTTCAGGAGTT[A/G]
AGTCTGGAGTGGAGTTGTGGAGCTGCCTAAACTCAGCTTCACAACTCTAGTTCATTTTGTGAGAGAGCTCCACCCAGCTCCACTCCCAGTTTTGGTGGAG

Reverse complement sequence

CTCCACCAAAACTGGGAGTGGAGCTGGGTGGAGCTCTCTCACAAAATGAACTAGAGTTGTGAAGCTGAGTTTAGGCAGCTCCACAACTCCACTCCAGACT[T/C]
AACTCCTGAAGTTAAATTTATGAGTTGGAGCTGTATCAAACATGCCCTAAAAGTACCAACCAAGGGGAGTGAAGAAACGGGCCTTCACCAGCTTTGCATT

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 52.00% 47.90% 0.06% 0.00% NA
All Indica  2759 32.20% 67.70% 0.04% 0.00% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 39.30% 60.70% 0.00% 0.00% NA
Indica II  465 19.80% 80.20% 0.00% 0.00% NA
Indica III  913 34.60% 65.30% 0.11% 0.00% NA
Indica Intermediate  786 31.40% 68.60% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 45.60% 52.20% 2.22% 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
vg0208132368 A -> G LOC_Os02g14730.1 upstream_gene_variant ; 2993.0bp to feature; MODIFIER silent_mutation Average:79.938; most accessible tissue: Zhenshan97 panicle, score: 98.827 N N N N
vg0208132368 A -> G LOC_Os02g14720-LOC_Os02g14730 intergenic_region ; MODIFIER silent_mutation Average:79.938; most accessible tissue: Zhenshan97 panicle, score: 98.827 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)
vg0208132368 A G -0.03 -0.01 -0.01 -0.08 -0.05 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208132368 NA 3.08E-10 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0208132368 NA 4.37E-06 mr1171 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
vg0208132368 NA 1.56E-18 mr1557 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
vg0208132368 NA 5.21E-08 mr1570 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
vg0208132368 NA 3.52E-06 mr1570 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
vg0208132368 6.31E-08 1.63E-09 mr1570_2 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