I have a pileup file from calling samtools mpileup and I'm confused to see a "]" in the column that shows read-base agreement with reference.
1 861225 G 45 ............................................^]. ;JKKKKKKKKKKKKKKKKFJ7FKKJKJKKKIKIJKKKKKHGJHE9
Reading the documentation, I don't see mention of "]" as an option. Only "." "," and "atgc"