Hi all, was wondering what does it mean by secondary alignment in BAM flag?

What is been defined as unmapped reads?

**Option used**:

    samtools view -F 260 bam_file

Thanks!
Unmapped reads are in the BAM file but have no valid assigned position (N.B., they may have an assigned position, but it should be ignored). It's typically the case that a number of reads can't be aligned, due to things like sequencing errors, imperfect matches between the DNA sequenced and the reference, random e. coli or other contamination, etc..

A secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary".