Difference between Alignment quality and Mapping quality

Question

[ammarsabir15]

I want to ask is there any difference between alignment quality and mapping quality of BAM file ??

Answer 1

[jh.monin]

Alignment score is the quality of of matching between the read-sequence and reference-sequence. Mapping quality is the confidence that the read is correctly mapped to the genomic coordinates. For example, a read may be mapped to several genomic locations with almost a perfect match in all locations. In that case, alignment score will be high but mapping quality will be low.