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Detailed information for vg0314207934:

Variant ID: vg0314207934 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 14207934
Reference Allele: GCGCCGCCGCCGC	Alternative Allele: GCGC,GCGCCGCCGCCGCCGCCGC,G
Primary Allele: GCGCCGCCGCCGC	Secondary Allele: GCGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTCCTCGTCTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAAGAGTACGCACTTAGCTATAGCTAGCTCCGGCCACATCTCCGTTTCC[GCGCCGCCGCCGC/GCGC,GCGCCGCCGCCGCCGCCGC,G]
CGCCGCCGCCGGCACAAACTGACCGATTCGATCCATGTCCATATTGTGCAGGGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGG

Reverse complement sequence

CCGATGGCGATCTTCAGACGCGTGCCCCACGGCACCGTCGCCGATATCCCTGCACAATATGGACATGGATCGAATCGGTCAGTTTGTGCCGGCGGCGGCG[GCGGCGGCGGCGC/GCGC,GCGGCGGCGGCGGCGGCGC,C]
GGAAACGGAGATGTGGCCGGAGCTAGCTATAGCTAAGTGCGTACTCTTGAAGAGGTGGTTCTCGAGGCTGCCGCGCGGCATGAACTCGTAGACGAGGAGG

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.