Methylation color in igv

[Kate Park]

I have PacBio HiFi reads with MM and ML tags indicating base modifications. When I open the BAM file in IGV and set Color alignments by → Base modification → 2-color (5mC), all modified bases appear blue (as shown in image 1).  


 Upon closer inspection, I noticed that the coloring behavior differs depending on whether I select Base modification (5mC) or 2-color (5mC). In the 2-color mode, bases with  base modification:5mC 74% were colored in dark blue not red.  (images 2 and 3)).  

  I've also attached my Color Legend settings (image 4) and Preferences → Alignment Track Default settings (image 5) for reference.  
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My goal is to clearly distinguish methylated and unmethylated bases using red and blue coloring.
What settings or adjustments can I make in IGV to achieve this?  

[igv-help]

Hi,  base modification display is described here: https://igv.org/doc/desktop/#UserGuide/tracks/alignments/base_modifications/.      The "Color Legends" do not apply to base modifications,  that is for an older technology.  Sorry for the confusion.   

Please confirm that you have chosen 2-color mode if that is what you are looking for.    In two color mode a base with 5mC modification likelihood > 50% should be red.  If its not I don't really have an explanation, and would probably need to see a data sample to comment further.