Importing CSV files with taxonID,count seems to result in wrong assignments, though taxonName,count works.
For example, if I import the following file:
All is ok. Then if I export the file as taxonID,count I get:
All is still ok. However, if I then re-import this file into MEGAN6.10.5 (and earlier versions), the reads are incorrectly assigned to bacteria instead of the correct eukaryotic species.