bwa mapped, interesting SAM output

[mo_hit4u]

Hi,

I masked a sequence using repeatmasker, where it replace regions with 'N' which it wanted to masked. After that I used bwa to map reads back to sequence. SAMTOOL displayed some region of sam file as following:

SRR329951.3160235 16 * 1 37 99M * 0 0 ATGATCTACCCATTGTTACATGAGTGTGGTTTCAACACTACTCTGTATATAGAGACACATTTATGTCCACATCTTAAACGTCTAGTCCTTCTAGGTGTT CCC##########CCC3CCCCCCACC?CAB@:AB?CCCCBCCDCCCBCCDACC=CCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i

In the second column it idicates that sequence being reverse complemented and third column indicates that it is mapping to "*" or undefined region.
can anybody suggest what this could mean or if you have experienced the same then tell me the reason why this could have occur?

[xied75]

http://samtools.sourceforge.net/SAM1.pdf

RNAME: Reference sequence NAME of the alignment. If @SQ header lines are present, RNAME
(if not `*') must be present in one of the SQ-SN tag. An unmapped segment without coordinate
has a `*' at this eld. However, an unmapped segment may also have an ordinary coordinate
such that it can be placed at a desired position after sorting. If RNAME is `*', no assumptions
can be made about POS and CIGAR.