mate strands in IGV

[tahamasoodi]

Hi,

Are mate strands of Illumina Hiseq complementary to each other? What I see in IGV, the sequence in both the mate strands (forward and reverse) is totally different?
Can anybody through more light on this?

Thanks,

[swbarnes2]

The two ends of a paired end read should not cover the same sequence. They are two ends of a single DNA fragment, and they should not overlap. They can, but that's a waste of sequencing.

Especially if you really mean mate-pairs, which are generated in a more complicated library prep, so that the inert sizes are much larger than with normal paired end reads.

[tahamasoodi]

If they are two ends of a single fragment, that means they should align at the same position of the reference genome. But what I see in my sample at many places when I color the reads in IGV based on insert size, some reads are present in e.g. chromosome 4 and when I search their mate, it is present in some other chromosome and the interesting thing is that both the reads have the same sequence as the reference.