BBMap supports extensive quality-related output histograms. For example:

bbmap.sh ref=hg19.fa in1=read1.fq in2=read2.fq mhist=mhist.txt ihist=ihist.txt ehist=ehist.txt qhist=qhist.txt qahist=qahist.txt indelhist=indelhist.txt

...and various others. That will generate the files mhist.txt, which shows the rates of match, substitution, insertion, deletion, and N at each base position; ihist, the insert size histogram; and so forth (they're documented in the shell script). They're all tab-delimited columns, so they're easy to plot in R or Excel.

Thank you Guys. I found "Qualimap" is a good software for knowing the quality of Alignment run. The reference article is here.