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Detailed information for vg0314208825:

Variant ID: vg0314208825 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 14208825
Reference Allele: GCAlternative Allele: G,AC
Primary Allele: GCSecondary Allele: G

Inferred Ancestral Allele : GC (evidence from allele frequency in Oryza rufipogon: GC: 0.99, G: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGCGCCGAGGTCAGAGGCGCCGGCTCCGGCGGCGGCGCGGCCTCGCGGCGGCGGAGCGCCTCCGCCAAGCTGCCCTGATCGCCCGCGTGCGTTCGTGG[GC/G,AC]
GCGCCACGTCATCGCGAGTACGTATTTGTATACGTGTACGTGTGTGTATATACTTTAGCTGCTGTATAAGATGGCACGGCCGATGTATTGTACGTGGTGA

Reverse complement sequence

TCACCACGTACAATACATCGGCCGTGCCATCTTATACAGCAGCTAAAGTATATACACACACGTACACGTATACAAATACGTACTCGCGATGACGTGGCGC[GC/C,GT]
CCACGAACGCACGCGGGCGATCAGGGCAGCTTGGCGGAGGCGCTCCGCCGCCGCGAGGCCGCGCCGCCGCCGGAGCCGGCGCCTCTGACCTCGGCGCGGA

Allele Frequencies:

Allele Effect:

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.