I don't understand in samtools tview the signification of an underlined read.

I understand what orphan means (in paired end, the other pair end is not mapped), but what secondary means? it means it's a duplicate ? Sometimes I can have two reads with the same name underlined and I don't know how to analyze them.

I found [Here][1] somebody talking about tview legend but it's not clearly explain for underlined reads.

Thanks

 [1]: https://www.biostars.org/p/13299/
<p><strong>Secondary</strong>: the read was mapped elsewhere (primary location). This position is another candidate position for this read.</p>
