I have a multiple samples and I run mapping with Bowtie2 for them and now I have .bam files. I have tried to run Multiqc to see how is mapping rate, duplication rate and other features but It did not work with bowtie output I think. 
I would like to know is there any graphical program like Multiqc for observing aligning features?
MultiQC doesn't extract information from the bam files, rather, it extracts from log files. Bowtie2 logs are output to stderr, you have to redirect them to a file and pass this file to MultiQC.