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Detailed information for vg0620421679:

Variant ID: vg0620421679 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20421679
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGAGCGGCGCAAGGAGGAGACAGGTCATTGGATGAGGTGGGCGGCGACGGCGATGGTAGGGAGGCTGGTGGAGACGAGGCGTCAGCGGCAAGGAGATC[G/A]
ATGGGGGCCGGGCGACGAGTCCTTTAGATCCGCCCTCCGTGCCCTCGCCTCGCACGTCGCCCACCGCCGTGGCCTTCCGCCCACCTCTCCCGCCGTCGAC

Reverse complement sequence

GTCGACGGCGGGAGAGGTGGGCGGAAGGCCACGGCGGTGGGCGACGTGCGAGGCGAGGGCACGGAGGGCGGATCTAAAGGACTCGTCGCCCGGCCCCCAT[C/T]
GATCTCCTTGCCGCTGACGCCTCGTCTCCACCAGCCTCCCTACCATCGCCGTCGCCGCCCACCTCATCCAATGACCTGTCTCCTCCTTGCGCCGCTCCAC

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 84.90% 14.60% 0.23% 0.19% NA
All Indica  2759 78.20% 21.20% 0.36% 0.25% NA
All Japonica  1512 93.70% 6.20% 0.07% 0.07% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 78.10% 21.70% 0.22% 0.00% NA
Indica III  913 61.30% 37.90% 0.44% 0.33% NA
Indica Intermediate  786 84.60% 14.20% 0.64% 0.51% NA
Temperate Japonica  767 93.50% 6.30% 0.13% 0.13% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 86.70% 13.30% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620421679 G -> A LOC_Os06g35070.1 upstream_gene_variant ; 4446.0bp to feature; MODIFIER silent_mutation Average:84.334; most accessible tissue: Zhenshan97 panicle, score: 93.936 N N N N
vg0620421679 G -> A LOC_Os06g35080.1 downstream_gene_variant ; 1727.0bp to feature; MODIFIER silent_mutation Average:84.334; most accessible tissue: Zhenshan97 panicle, score: 93.936 N N N N
vg0620421679 G -> A LOC_Os06g35090.1 downstream_gene_variant ; 1140.0bp to feature; MODIFIER silent_mutation Average:84.334; most accessible tissue: Zhenshan97 panicle, score: 93.936 N N N N
vg0620421679 G -> A LOC_Os06g35080-LOC_Os06g35090 intergenic_region ; MODIFIER silent_mutation Average:84.334; most accessible tissue: Zhenshan97 panicle, score: 93.936 N N N N
vg0620421679 G -> DEL N N silent_mutation Average:84.334; most accessible tissue: Zhenshan97 panicle, score: 93.936 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)
vg0620421679 G A -0.02 -0.01 -0.01 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620421679 1.83E-06 1.83E-06 mr1477_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
vg0620421679 NA 3.94E-07 mr1567_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
vg0620421679 1.61E-07 1.61E-07 mr1806_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
vg0620421679 NA 1.86E-07 mr1827_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
vg0620421679 6.17E-06 6.17E-06 mr1971_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