Hello

I have a few of questions while studying tool MARKDUPLICATES metrics file.

A list of `SECONDARY_OR_SUPPLEMENTARY_RDS` is there.

I know SECONDARY READS, but I am wondering about SUPPLEMENTARY READS.

Thanks in advance for full explanation.
Section 1.2 "Terminologies and Concepts" of the [SAM file format specifications][1] explain this:

> Chimeric alignment
>
>An alignment of a read that cannot be represented
> as a linear alignment. A chimeric alignment is represented as a set of
> linear alignments that do not have large overlaps. Typically, one of
> the linear alignments in a chimeric alignment is considered the
> “representative” alignment, and the others are called “supplementary”
> and are distinguished by the supplementary alignment flag. All the SAM
> records in a chimeric alignment have the same QNAME and the same
> values for 0x40 and 0x80 flags (see Section 1.4). The decision
> regarding which linear alignment is representative is arbitrary.


  [1]: https://samtools.github.io/hts-specs/SAMv1.pdf