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?
mpileup is originally made to call variants.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.