Does bwa support SOLiD PE data?

[2007lab]

Hi,
I have used 'bwa aln' and 'bwa sampe' for mapping Exome captured SOLiD PE reads.
I am getting very low PE mapping % (29-35%) One of the notes on the 'bwa version 0.5.9-r16' says:
Notes:
1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.
2. For reads shorter than 30bp, applying a smaller -o is recommended to
to get a sensible speed at the cost of pairing accuracy.

So my question is if bwa truly support SOLiD PE reads?
If so, what parameters have to be modified ?
The reads are F3 and F5, there is no R3.

Do the version 0.5.9-r16 have changes to sampe that was posted by Brugger at bwa-support mailing list.

CATEGORY TOTAL_READS PF_READS %_PF_READS PF_NOISE_READS PF_READS_ALIGNED %_PF_READS_ALIGNED
FIRST_OF_PAIR 134520572 134520572 1 34 14456389 0.107466
SECOND_OF_PAIR 134520572 134520572 1 17 82292274 0.611745
PAIR 269041144 269041144 1 51 96748663 0.359605

CATEGORY READS_ALIGNED_IN_PAIRS %_READS_ALIGNED_IN_PAIRS
FIRST_OF_PAIR 10169637 0.70347
SECOND_OF_PAIR 10169650 0.12358
PAIR 20339287 0.210228



Thanks
VJ