Hey everyone, and before anything else, thanks for the help!
I started working on a new project with low coverage dna seq. The project use .bam files and mpileup using samtools. After a lot of readings, i found out that the data uses sanger FASTQ mapping quality. Notice: i work on readings with no ref bases, if it changes anything.
I am trying to understand if there will allways be a reading map quality after the sign of a new read, which is to say: will it allways be in the format of '^XB' where X stands for the read quality and B stands for the base in the read?
Thanks again for the help, and if there is an older post about it, i will be happy if you can give me a link.
For example, my pileups look like that:
Chr_name pos ref 3 GG^]G etc...