So I am recently getting my foot in the door in using bedtools and I had a question about correct usage for my end goal

I am looking to essentially filter a BAM file for reads that only have 100% intersection on regions specified with a bed file.

  [====================BAM===================] (A)

                (-----------------)                          (-----------------------)      (B)

I would only want to pull down reads in A that have complete overlap of reads in B.

The command I am using is:

bedtools intersect -F 1.0 -a file.bam -b regions.bed

However when I run

samtools mpileup -l regions.bed file.bam

I see that there are inconsistencies in the depth at each of the positions in the regions. This doesn't quite make sense to me intuitively because I would expect an even depth across each position in the region because the intersect should filter out reads with incomplete coverage across the region.

Perhaps I am thinking of the usages of these tools wrong though and could definitely use some help in clarifying either inconsistencies in my intuition or commands that don't match my intentions.

Cheers!