I have a read where sam flag is 69 (meaning Pair End Read, Unmapped and First in Pair) , Mapping quality is 0 and Cigar string is `*`. The sequence is not showed in the viewer (samtool tiview,IGV).

I'm wondering why a read is said unmapped whereas a position is given in the sam file. So the read can be mapped? When I tried to align with blat, I found one unique position (the same as in sam file).

So I don't understand ...Why this read is said unmapped whereas a position is given(chr12 112036669)? How to retrieve/use this read in my bam to display in viewer as a "good sequence"? Why is the read filtered? Because of the mapping quality? and why CIGAR string is set to `*`? Can I use it of one way or an another or is it a better idea to let this read stay in "garbage"? Thanks.

    M02792:15:000000000-A98VA:1:1103:24705:18436 69 chr12 112036669 0 * = 112036669 0 GTCGCTGAAGCCCCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCCGCCGCCCGCGG CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG8FGGG@FF:F@FE=: RG:Z:A421
<p>If an alignment is marked as unmapped then any position information is unreliable, since it may simply be a hold-over from an internal method that didn&#39;t get cleared. In the case of paired-end reads like this, typically an unmapped mate is given the coordinates of its mapped mate.</p>
