Insert size in Sam files

[foxyg]

Hi,

I got a questions regarding the insert size in the sam files. In my understanding, the insert size is the size of the fragment measured by counting the distance between the starting locations of the pairend read. But sometimes, I notice there is negative insert size and sometimes a insert size over several thousand. How can I explain those insert size? I am using illumina pair end sequencing.

Thanks

[adamdeluca]

A negative insert size indicates that the reads overlap, your fragment was shorter than 2x read length.