Hi, I'm having some trouble understanding how and why the Uniqueness and Alignment used with the mapability feature can be discrepant if they seem to be measuring basically the same thing. And when they are discrepant, what might this suggest for that region? Additionally, I used the Self Chain function which was helpful, but again, did not seem to match with the mapability feature. Is there any way to use all three of these tools to determine with some certainty if a gene is or isn't homologous to another region in the genome?
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