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Detailed information for vg0421752849:

Variant ID: vg0421752849 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 21752849
Reference Allele: C	Alternative Allele: CAG,G
Primary Allele: C	Secondary Allele: CAG

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

ACAACCGCCTACAGATATACAGAAATTCCTCTCTTGTCAACAGCCTCTTTCCTCGTGGAGCCTTTCTATACTGTACAGTAAAATCAGATCGGTGTAGTAA[C/CAG,G]
AGAGTTACGACATGTTGCTGACATCTCTAACATTATATATCTACGATGTCATGGGAACAATTCTCCTGCTGAACATTCATCAGCACTCATGGATGACTGA

Reverse complement sequence

TCAGTCATCCATGAGTGCTGATGAATGTTCAGCAGGAGAATTGTTCCCATGACATCGTAGATATATAATGTTAGAGATGTCAGCAACATGTCGTAACTCT[G/CTG,C]
TTACTACACCGATCTGATTTTACTGTACAGTATAGAAAGGCTCCACGAGGAAAGAGGCTGTTGACAAGAGAGGAATTTCTGTATATCTGTAGGCGGTTGT

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.