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Detailed information for vg1128863871:

Variant ID: vg1128863871 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28863871
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGAGAGGGGGTTGGGCATGTGTGTCCCACCTACTAACTTAGCGAGTCAAGCGTGCTTAACCTGCTACGTTAATAGAAACCGCTTCCCAAATCATGGAA[G/A]
GAGTCGGTTAACACCGGCTTTTGAAGACCAGGGAGAGTTTTGCAGCCAAGAGAGACAATGTAATCATGAGCAAGAGATAAAGGAAGTAAAATAGACTTAC

Reverse complement sequence

GTAAGTCTATTTTACTTCCTTTATCTCTTGCTCATGATTACATTGTCTCTCTTGGCTGCAAAACTCTCCCTGGTCTTCAAAAGCCGGTGTTAACCGACTC[C/T]
TTCCATGATTTGGGAAGCGGTTTCTATTAACGTAGCAGGTTAAGCACGCTTGACTCGCTAAGTTAGTAGGTGGGACACACATGCCCAACCCCCTCTCTCC

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 88.20% 11.80% 0.04% 0.00% NA
All Indica  2759 91.60% 8.40% 0.04% 0.00% NA
All Japonica  1512 86.20% 13.70% 0.07% 0.00% NA
Aus  269 82.90% 17.10% 0.00% 0.00% NA
Indica I  595 96.00% 4.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 84.30% 15.70% 0.00% 0.00% NA
Indica Intermediate  786 92.00% 7.90% 0.13% 0.00% NA
Temperate Japonica  767 87.70% 12.30% 0.00% 0.00% NA
Tropical Japonica  504 85.90% 13.90% 0.20% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg1128863871 G -> A LOC_Os11g47850.1 downstream_gene_variant ; 2418.0bp to feature; MODIFIER silent_mutation Average:86.398; most accessible tissue: Zhenshan97 panicle, score: 97.067 N N N N
vg1128863871 G -> A LOC_Os11g47860.1 downstream_gene_variant ; 681.0bp to feature; MODIFIER silent_mutation Average:86.398; most accessible tissue: Zhenshan97 panicle, score: 97.067 N N N N
vg1128863871 G -> A LOC_Os11g47850-LOC_Os11g47860 intergenic_region ; MODIFIER silent_mutation Average:86.398; most accessible tissue: Zhenshan97 panicle, score: 97.067 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)
vg1128863871 G A 0.02 0.02 0.01 0.0 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128863871 1.22E-06 2.34E-08 mr1698_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
vg1128863871 NA 3.35E-06 mr1994_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