The documentation for samtools mpileup states under the -x, --ignore-overlaps-removal, --disable-overlap-removal option:

When enabled, where the ends of a read-pair overlap the overlapping region will have one base selected and the duplicate base nullified by setting its phred score to zero. It will then be discarded by the --min-BQ option unless this is zero.

I would appreciate some clarifications on the terminology here.

First, does --min-BQ filter bases using their BAQ or their original phred base quality score from the FASTQ file, assuming that BAQ is computed? I am assuming that BAQ is what is being used.

Second, does this mean that duplicate bases are nullified by setting their original base qualities (phred scores) in the SAM/BAM file to zero prior to BAQ computation? Or, is BAQ first computed and then duplicate bases are nullilfied by setting their BAQ scores to zero?