Alignment statistics from bwa?

[menenuh]

Hello, I am a newbie and I have a question,
Is it possible to get alignment statistics from sam output of bwa algorithm? And also, what happens to unaligned reads? Are there also present in the generated sam file? I have several 0's in the FLAG field in the sam output, is it an unmapped read?
Well, it seems like I have more than one question

[lh3]

You may get SAM output and then convert it to BAM. samtools flagstat will give you a brief stats. Unmapped reads are stored in the SAM file.