Hi All! I am new to bioinformatics and I am using mothur to analyze my 16s V4 sequencing data. I am analyzing between two sequencing runs (fall/winter and spring/summer). I noticed that when I run these two batches together and align them to the silva database, their start/ends are very different so screening and filtering steps break or cut out many of my samples.

What does drastically different start/ends between batches really mean? My sequence provider suggested that the two batch simply are different taxa in the SILVA database (like fall/winter is enriched in taxa different from spring/summer) but that doesn't really make sense to me because if we cut the silva database to the V4 region and all my samples r also only amplifying that region then why would they be different?

I have attached a screenshot of my summary from aligning both my batches to the silva database. Any insight would be extremely helpful as I have no one else in my lab to ask these questions and cannot find literature about this problem!

I trimmed the SILVA database to start=11894, end=25319