What is "unmapped read segments" in the output of samtools idxstats?
An unmapped read segment is any entry with bit 4 of the flag field set (i.e., it's unmapped). Assuming the reference to which you aligned reasonably matches the sample from which the reads were generated, less than ~10% of to total reads should be unmapped.
Please note that BAM files have no idea what a &quot;feature&quot; is. They only contain information about reads and the chromosomes/contigs to which they align.