I am trying to understand some details about alignment of sequencing reads and the alignment tags that are included in the output files in SAM format. I am using the STAR aligner and have the following question:
Will reads that map to multiple loci in the genome get assigned the same AS score and MD tag? In other words: Is the AS score/MD tag reported the maximum one obtained, i.e. for the best alignment of that specific read? I have browsed through some SAM files and it seems to be the case that different alignments of the same read have the same AS score and MD tag. But I wanted to double-check that I am understanding this correctly.