<p>Hi,</p>

<p>In the <a href='http://samtools.sourceforge.net/'>samtools</a> manual, for the DP4 field it states that the:</p>

<p>"...sum can be smaller than DP because low-quality bases are not counted."</p>

<p>I wonder, what is the cut-off for this? How low does the quality of a base need to be and what determines whether a base is low-quality?</p>

<p>Thanks,</p>

<p>Jon</p>

<p>This is the mpileup -Q option, which by default is 13.</p>
