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Detailed information for vg1204483091:

Variant ID: vg1204483091 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4483091
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCAAACGAATTAATTGTACGCGAGAATTCGAGATGCCACTTGTGTTAATTTAGAGCAATTAAGAGAGGCAACCACTACATAAAATTCAAGACAAAAAGA[G/A]
AGAGGGGAAGAGTAGATTAGCCAAACAAACATTGGGACTACTGTATTAGAATTAGTATAGATGTGATATATTGTATATGTTACCTCTATATTTATTAGTT

Reverse complement sequence

AACTAATAAATATAGAGGTAACATATACAATATATCACATCTATACTAATTCTAATACAGTAGTCCCAATGTTTGTTTGGCTAATCTACTCTTCCCCTCT[C/T]
TCTTTTTGTCTTGAATTTTATGTAGTGGTTGCCTCTCTTAATTGCTCTAAATTAACACAAGTGGCATCTCGAATTCTCGCGTACAATTAATTCGTTTGGA

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 94.30% 5.70% 0.00% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 47.20% 52.80% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 90.10% 9.90% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1204483091 G -> A LOC_Os12g08750.1 upstream_gene_variant ; 3437.0bp to feature; MODIFIER silent_mutation Average:82.967; most accessible tissue: Zhenshan97 young leaf, score: 93.68 N N N N
vg1204483091 G -> A LOC_Os12g08750-LOC_Os12g08760 intergenic_region ; MODIFIER silent_mutation Average:82.967; most accessible tissue: Zhenshan97 young leaf, score: 93.68 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)
vg1204483091 G A -0.01 -0.01 -0.01 -0.01 0.0 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204483091 2.18E-06 NA mr1095 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
vg1204483091 NA 5.07E-11 mr1180 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
vg1204483091 NA 1.71E-08 mr1260 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