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Detailed information for vg0216000792:

Variant ID: vg0216000792 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16000792
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCCCTTCCCGTCCCGGCGATGGAGGCGGCGGCGCAAGGGGAGGTCAAGACCCCCGCGCTTTGCTCCGCGCACATGATGTCCTGGTCACCTTCGCTGG[A/C]
AGGGGCGCCGAGGTGGAGATGGGAGCGGAGCACGGCGAGGCGCCGCGATAGCGACATTTGTGTGGGAGACAAGGTGGGGATGAAAGCGTGGTCTATGGAC

Reverse complement sequence

GTCCATAGACCACGCTTTCATCCCCACCTTGTCTCCCACACAAATGTCGCTATCGCGGCGCCTCGCCGTGCTCCGCTCCCATCTCCACCTCGGCGCCCCT[T/G]
CCAGCGAAGGTGACCAGGACATCATGTGCGCGGAGCAAAGCGCGGGGGTCTTGACCTCCCCTTGCGCCGCCGCCTCCATCGCCGGGACGGGAAGGGAAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.50% 9.80% 0.66% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 67.90% 30.10% 2.05% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 40.90% 55.70% 3.39% 0.00% NA
Tropical Japonica  504 97.40% 2.00% 0.60% 0.00% NA
Japonica Intermediate  241 91.70% 7.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0216000792 A -> C LOC_Os02g27190.1 missense_variant ; p.Glu27Ala; MODERATE nonsynonymous_codon ; E27A Average:91.294; most accessible tissue: Zhenshan97 flower, score: 96.642 unknown unknown TOLERATED 0.56

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)
vg0216000792 A C -0.04 -0.02 0.01 0.02 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216000792 NA 1.95E-06 mr1627 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
vg0216000792 NA 3.33E-10 mr1627_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