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Detailed information for vg0505753938:

Variant ID: vg0505753938 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5753938
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAATATTCATGATAGCTAGTTAAAAAAAATTAAAACATTGATTTGTTCATTGTCCTGCTGAATGGGCTTCATGCACGTGGGAGCACTTTCGCTGATAGTG[G/A]
CACGTTGCAACACGCTGCGTGTTGGATAGTAGTTCTCAAATATAGTATAATTTTTAACACAAAACAAATATATTATCAAAATATATTTAATGTTAGATTT

Reverse complement sequence

AAATCTAACATTAAATATATTTTGATAATATATTTGTTTTGTGTTAAAAATTATACTATATTTGAGAACTACTATCCAACACGCAGCGTGTTGCAACGTG[C/T]
CACTATCAGCGAAAGTGCTCCCACGTGCATGAAGCCCATTCAGCAGGACAATGAACAAATCAATGTTTTAATTTTTTTTAACTAGCTATCATGAATATTC

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 52.00% 47.40% 0.59% 0.00% NA
All Indica  2759 19.80% 79.30% 0.94% 0.00% NA
All Japonica  1512 98.50% 1.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 19.80% 78.30% 1.85% 0.00% NA
Indica II  465 15.30% 83.90% 0.86% 0.00% NA
Indica III  913 17.10% 82.90% 0.00% 0.00% NA
Indica Intermediate  786 25.60% 73.00% 1.40% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 66.70% 31.10% 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
vg0505753938 G -> A LOC_Os05g10570.1 downstream_gene_variant ; 2915.0bp to feature; MODIFIER silent_mutation Average:64.034; most accessible tissue: Callus, score: 89.566 N N N N
vg0505753938 G -> A LOC_Os05g10580.1 downstream_gene_variant ; 2566.0bp to feature; MODIFIER silent_mutation Average:64.034; most accessible tissue: Callus, score: 89.566 N N N N
vg0505753938 G -> A LOC_Os05g10570.2 downstream_gene_variant ; 2915.0bp to feature; MODIFIER silent_mutation Average:64.034; most accessible tissue: Callus, score: 89.566 N N N N
vg0505753938 G -> A LOC_Os05g10570-LOC_Os05g10580 intergenic_region ; MODIFIER silent_mutation Average:64.034; most accessible tissue: Callus, score: 89.566 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)
vg0505753938 G A 0.25 0.21 0.16 0.11 0.18 0.19

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505753938 NA 6.36E-06 mr1816 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
vg0505753938 4.54E-06 1.04E-06 mr1816 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