Hi, I used samtools  to generate a mpileup file. In the base column, I notice some "!".  I sought out the sigification in domcumentation/already asked question and haven't find their meaning. Does anybody know?

Exemple:

FNXXX	2595	T	1	^!a	J


Try to add ```-Bx``` to your command.

Short story long:

mpileup is originally made to call variants. To not count the overlapping bases between the forward and reverse reads twice samtools changes the quality score to "!". This "!" has a phred score of 0 and will be ignored in the variant calling process.

Here more info:
https://sourceforge.net/p/samtools/mailman/message/32793789/