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Detailed information for vg0609116057:

Variant ID: vg0609116057 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9116057
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CGCAGGGGAGAGGAGGGATGCCAAGGAGAAGATGTCACGGGAGAGGAAGAGGACGTGCGGTGAGGGAGAGATGTGGGGTGCTGTGAGGGAGGAGGGAGGC[A/G]
GGAGAGGAGGGCCGTCAGGAGAAGAGGGGCTGCGGGTAGGGGGAGCGTGTGGAGATCAGGGCACCGGTAGGGGGAGAGAGGCGGAAGCGGAGAGGGGAGG

Reverse complement sequence

CCTCCCCTCTCCGCTTCCGCCTCTCTCCCCCTACCGGTGCCCTGATCTCCACACGCTCCCCCTACCCGCAGCCCCTCTTCTCCTGACGGCCCTCCTCTCC[T/C]
GCCTCCCTCCTCCCTCACAGCACCCCACATCTCTCCCTCACCGCACGTCCTCTTCCTCTCCCGTGACATCTTCTCCTTGGCATCCCTCCTCTCCCCTGCG

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 70.90% 20.60% 6.86% 1.71% NA
All Indica  2759 58.40% 31.00% 7.76% 2.86% NA
All Japonica  1512 86.00% 7.10% 6.88% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 45.00% 40.30% 12.77% 1.85% NA
Indica II  465 79.10% 5.40% 11.40% 4.09% NA
Indica III  913 52.20% 44.20% 1.31% 2.19% NA
Indica Intermediate  786 63.40% 23.70% 9.29% 3.69% NA
Temperate Japonica  767 74.10% 12.60% 13.30% 0.00% NA
Tropical Japonica  504 98.80% 1.00% 0.20% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 82.20% 8.90% 6.67% 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
vg0609116057 A -> G LOC_Os06g16020.1 upstream_gene_variant ; 630.0bp to feature; MODIFIER silent_mutation Average:83.936; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0609116057 A -> G LOC_Os06g16030.1 upstream_gene_variant ; 887.0bp to feature; MODIFIER silent_mutation Average:83.936; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0609116057 A -> G LOC_Os06g16010.1 downstream_gene_variant ; 3172.0bp to feature; MODIFIER silent_mutation Average:83.936; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0609116057 A -> G LOC_Os06g16020-LOC_Os06g16030 intergenic_region ; MODIFIER silent_mutation Average:83.936; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0609116057 A -> DEL N N silent_mutation Average:83.936; most accessible tissue: Zhenshan97 panicle, score: 90.849 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)
vg0609116057 A G -0.07 -0.03 -0.04 -0.06 -0.06 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609116057 1.44E-10 2.43E-09 Awn_length Jap_All YES 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
vg0609116057 4.89E-06 3.78E-11 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
vg0609116057 3.90E-07 1.60E-10 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
vg0609116057 3.52E-09 1.89E-12 mr1570_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
vg0609116057 NA 5.26E-08 mr1709_2 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
vg0609116057 NA 3.75E-06 mr1757_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