Question about First in pair and Second in pair reversed.

[Martino]

At the moment, I am using IGV for my internship. I am using it for finding structural rearrangements.

 

But there is something in IGV I don't understand.

 

This is about the reads, when a read is a 'First in pair' and the other read is 'Second in pair'. This is from left to right.

 

Sometimes, I see that those in reverse. When I do a mouse move over, I see 'Second in pair' before 'First in pair'. I would think this could be an inversion, but IGV itself it is not. According to IGV, it is a normal concordant pair and NOT a discordant pair.

 

My question is: What is the reason of the fact that some concordant pairs are in opposite direction in IGV? So, that the first read says it is the 'Second in pair' and the second read is the 'First in pair'.

Does it have something to do with the platform on which the subject genome had been sequenced? I read something about on the website.

Or does it mean that that fragment has been from the reverse strand of the subject genome?

[Jim Robinson]

Hi Martino,

This might best be posed in an analysis forum like SeqAnswers,  but the short answer is the "rules" depend on you platform and library.  For common Illumina libraries pairs are expected to be "inward facing" when aligned to the genome,  which simply means the "leftmost" read should point to the right while the "righmost" read to the left.   This has nothing to do with first or second in pair,  that refers to which end was sequenced first. 

Jim