The classification result is visualized in the “MaChIAto_alignment_pie_chart.png”
“MaChIAto_alignment_pie_chart.png” has the following labels:
- Unmodified: The unedited amplicon sequence
- Perfect Editing: The edited sequence that a user intended to generate (e.g., precise knock-in sequence, expected substitution/deletion/insertion…)
- Imperfect Editing: The sequence that is simular to “Perfect Editing” sequence. However, the junction sequence is imperfect.
*The class is specilized for the homology-based knock-in. In knock-out and Prime Editing, the “Imperfect Editing” reads can be condidered as just InDels.
InDels: The sequence that has a trace of editing (e.g., deletion/insertion/frequent substitutions) around the target site. - Deletion: The InDel sequence whose length is less than that of the unedited amplicon sequence
- Insertion: The InDel sequence whose length is more than that of the unedited amplicon sequence
- Frequent substitutions: The InDel sequence whose length is equal to that of the unedited amplicon sequence
UC: Unclear sequence that has the insufficient information to be recognized as the focusing sequence. - UC (Ambiguous Editing): There is the expected sequence (e.g., knock-in cassette and Reverse transcript). However, the information of the end of amplicon is unclear. For example, The edited reads, which do not have the site of complementary strand nicking, are classified into this class.
- UC (Others): There is not enough sequence informaton for the classification. The unedited amplicon read with sequence errors and read amplified from the other locus can be classified into the this class.