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Detailed information for vg0223652746:

Variant ID: vg0223652746 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23652746
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTTGCTGGTGATGGTGGGAGAGATCGCCGCGAACAGGCCGCGAACAGGAGGTCGTAGCGCCGCGCGGACGTCGGGCGCATGATGACCGGCGTGGTGGA[G/C]
TCGGTGGTGCTCGTACCAGAGGTGGTGCGGTCGCGTGGTGAGCGCGGCGAGGGAGGTGCTCGAGATGAGCGCGACGCGGGTGGTGATCCCGGGCAACTTC

Reverse complement sequence

GAAGTTGCCCGGGATCACCACCCGCGTCGCGCTCATCTCGAGCACCTCCCTCGCCGCGCTCACCACGCGACCGCACCACCTCTGGTACGAGCACCACCGA[C/G]
TCCACCACGCCGGTCATCATGCGCCCGACGTCCGCGCGGCGCTACGACCTCCTGTTCGCGGCCTGTTCGCGGCGATCTCTCCCACCATCACCAGCAAGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.70% 16.30% 0.02% 0.00% NA
All Indica  2759 77.20% 22.80% 0.04% 0.00% NA
All Japonica  1512 97.10% 2.90% 0.00% 0.00% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 85.70% 14.30% 0.00% 0.00% NA
Indica II  465 79.10% 20.90% 0.00% 0.00% NA
Indica III  913 69.30% 30.60% 0.11% 0.00% NA
Indica Intermediate  786 78.80% 21.20% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 93.50% 6.50% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0223652746 G -> C LOC_Os02g39155.1 missense_variant ; p.Glu7Asp; MODERATE nonsynonymous_codon ; E7D Average:94.254; most accessible tissue: Zhenshan97 young leaf, score: 99.462 unknown unknown DELETERIOUS 0.00

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)
vg0223652746 G C 0.0 0.0 0.02 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223652746 NA 1.56E-06 mr1060_2 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