Hello, I'm working with paired end rna-seq data so two fastq files produced 1 BAM file. I know col 10 represent the seq and col 11 have its ascii code for quality. If the original seq length 100bp when I extracted some seq from BAM file I noticed some reads of length LESS than the original length. For example in one location one seq has cigar (40M, which means 40 bps matched) my question is: what happened to the rest of the seq (60bps)?? Another point, in this case we have paired end data which means two seq one from each end but BAM file has only one. This one included in BAM file to which end belongs??