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