SAM flag

Question

[tea.vuki]

Hello, I have a question regarding 0x0002 flag - the read is mapped in a proper pair. When read is mapped in a proper pair, does that mean that both pairs are aligned to the same contig?

Answer 1

[Pierre Lindenbaum]

, does that mean that both pairs are aligned to the same contig?

well the formal definition of properly paired is:

each segment properly aligned according to the aligner

but yes, 99.999% it means than both reads of a pair are mapped on the same chromosome, with a different strand (FR), at a "good" distance from each other.

[tea.vuki]

Thank you!