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5mC coloring mode
This coloring scheme was designed to provide visualization of 5-Methylcytosine (5mC) modifications specified with MM/ML tags that is consistent with visualization of methylation from bisulfite sequencing. In this scheme color for modified bases is assigned based on the probability of the modification. Specifically:
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Base modifications with probability < 50% are colored blue
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Base modifiations with probility > 50% are colored red
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In both cases alpha transparency is applied with the degree of transparency proportional to the distance of probability from 50%. So base modifications with probability 0% are solid blue, base modifications with probability of 100% solid red, with increasing alpha shading applied in both cases as probability approaches 50%
Red bases indicate probability of 5-Methylcytosine (5mC) modification > 50%, blue indicate probability of 5mC modification < 50%.