mapping rates from BWA

You can run bamtools stats -in path/to/your/alignments.bam, which will (quickly) report general alignment statistics.

You can also run bamtools filter -isMapped false -in path/to/your/alignments.bam > unmapped.bam (or something quite close to that) to get your unmapped reads.

http://www.biostars.org/p/10763/

you can tell from the sam file, by checking the flags, or make the file into a .bam with samtools, and use flagstat from samtools to count.