Samtools tview : what does underlined reads mean ? Secondary or Orphan

Question

[ZheFrench]

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 somebody talking about tview legend but it's not clearly explain for underlined reads.

Thanks

Answer 1

[Pierre Lindenbaum]

Secondary: the read was mapped elsewhere (primary location). This position is another candidate position for this read.

[Shicheng Guo]

multiple alignment?