BaseModViewer
Modified bases are annotated using the MM (Modification Map) and ML (Modification Likelihood) tags within BAM files.
The MM tag describes which bases in the sequence are modified and provides the type of modification. It follows a pattern like MM:Z:C+m,5,12,0;, where the first base (e.g., 'C') indicates the base type, the sign ('+') indicates the strand, and the subsequent numbers indicate the positions of the modified bases.
The ML tag provides the modification probability, which is encoded as an array of values ranging from 0 to 255 - a 100% likelihood would be 255/255 and a 0% likelihood would be 0/255.
PacBio sequencing technologies use the kinetics of DNA polymerase during sequencing (specifically the duration of base incorporation and pauses between base incorporation) to detect and call these modifications. Methylated bases act as a molecular speed bump slowing down the polymerase and base incorporation. After data processing with bioinformatic software, this information is then stored as MM/ML tags in the BAM files.
Enter a line from your own data or click the example to see how these tags work. Can you find the CG methylation island and the Fiber-Seq 6mA open chromatin region in the example provided?