Quality metrics of the alignment (number of reads, coverage, GC-content, etc.) is assessed with QualiMap Bam QC (Galaxy version 2.2.2).
Reference: Okonechnikov, K., Conesa, A., & Garcı́a-Alcalde, F. (2015). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics, 32(2):292-4. doi: 10.1093/bioinformatics/btv566