l am a starters ,l'm reading "Reference flow: reducing reference bias using multiple population genomes".Have a question about the Merging and lifting. "For reads that aligned to more than one reference, we must choose a single “best” alignment to include in the ultimate SAM output. We select by choosing the alignment with the highest alignment score; roughly, this corresponds to the alignment with the fewest mismatches and gaps. "

This "score” refers to mapq？how can l get the best alignment?

thanks for your reply.