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Detailed information for vg0220740098:

Variant ID: vg0220740098 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20740098
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, G: 0.34, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTGGAGCAGAAGTAATCCTTGGTCCTGATCCTTTTCGTGCCAGTAAAGTAGGACTGCTTCCCCTTTCGGATACTGAACCCCATGCGGTGCCCATAGTC[A/G]
CAGTACAGCTTGTACGCCGCCTCCTCGCTGTACACTACCTTGCGGAGTAGTTCCTCGGTGCCCTCCTTGCTGCCATGAACCGTTGCTGCCTCTTCAGTCT

Reverse complement sequence

AGACTGAAGAGGCAGCAACGGTTCATGGCAGCAAGGAGGGCACCGAGGAACTACTCCGCAAGGTAGTGTACAGCGAGGAGGCGGCGTACAAGCTGTACTG[T/C]
GACTATGGGCACCGCATGGGGTTCAGTATCCGAAAGGGGAAGCAGTCCTACTTTACTGGCACGAAAAGGATCAGGACCAAGGATTACTTCTGCTCCAAGG

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 72.40% 27.60% 0.00% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 26.10% 73.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 97.40% 2.60% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 27.90% 72.10% 0.00% 0.00% NA
Tropical Japonica  504 21.80% 78.20% 0.00% 0.00% NA
Japonica Intermediate  241 29.50% 70.50% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg0220740098 A -> G LOC_Os02g34590.1 synonymous_variant ; p.Cys107Cys; LOW synonymous_codon Average:78.032; most accessible tissue: Zhenshan97 young leaf, score: 88.637 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)
vg0220740098 A G 0.01 0.01 0.03 0.01 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220740098 4.43E-06 1.09E-11 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652