What is the value of the insert size ?

[Taalouane]

What is the value of the insert size ?

[brentp]

So "insert-size" is actually the inside measurement and fragment length is the outside measurement.

So qualimap is reporting fragment length of 366 and indexstats is reporting 376.86.

Note that from goleft, insert_mean=86.96 and template_mean=376.86 which makes sense since your reads are about 150 bases each so we expect about 300 bases difference. (template_mean == fragment_length).

[Taalouane]

Thank you for your quick reply !!