Thanks brentp, solve my question mark on weird flagstats. However, regarding "reverse-complement your F5 reads (and reverse the quality)" as you mentioned, can I know how to reverse the reads?

just reverse complement the reads. You can do this with bioperl or biopython. In perl, it's like my $rc = reverse(seq); =~ tr/ACGTacgt/TGCAtgca/. So just loop over the csfasta and do that to every other line. And for the qual file. Just reverse it.

SOLiD reads are colourspace reads where I cant perform reverse complement on them, are there any other ways?

Oh, yes of course. I think in colorspace, you can just reverse the colorspace sequence, without complementing to get (what would be in base-space) the reverse complement. I havent mapped F3/F5 Solid reads but maybe check the -c parameter to bwa (http://bio-bwa.sourceforge.net/bwa.shtml)

I'm not sure whether this works, will give a try, thanks for the suggestions brentp, but I'm still hoping for a more concrete solution, perhaps other software may help

Yaira, it seems there's no concrete solution for bwa paired end mapping yet since bwa assumes paired end mapping has the same orientation as mate pair, maybe you can consider trying out Bioscope or try using bfast http://seqanswers.com/forums/showthread.php?t=7100 or bowtie http://bowtie-bio.sourceforge.net/manual.shtml#paired-end-colorspace-alignment