Command line output interpretation

1

Hi,
I’m relatively new to Megan,
I would like to know what the ‘with hits’ and ‘alignments’ output is referring to in the command line output of Megan.

Example:
Total reads: 38,168,423
with hits: 38,168,423
alignments: 490,239,242
Assign. Taxonomy: 35,523,332
Assign. KEGG : 14,485,325

Thanks!

2

With hits: how many reads have at least one alignment
If the alignment tool only passes on reads that have alignments, then with hits will equal the total number of reads.

Alignments: the total number of alignments