I believe I found a Bug in MEGAN6.
If I import from a CSV-File with only the following line as content (minimal example):
Salmonella entrica, 25
And choose for a new File: Import -> CSV Import then choose the file containing the above line and select in the following import window: "Class, Count(,Counts...)" and "Comma" and click only "Taxonomy" and "Apply" it then MEGAN assigns the 25 reads to "Salmonella enterica subsp. enterica serovar Typhimurium str. LT2-4_delta.ramA-kan" which cannot be correct since the reads should be assigned to "Salmonella entrica" and not a subspecies of it.
Can you confirm that? Or am I doing something wrong?
I'm currently using MEGAN6.1.11alpha Ultimate Edition .