Paired-end read layout, from http://thegenomefactory.blogspot.com/2013/08/paired-end-read-confusion-library.html

10_fragment_layout.txt

# Normal layout of a healthy read-pair.

fragment                  ========================================
fragment + adaptors    ~~~========================================~~~
SE read                   --------->
PE reads                R1--------->                    <---------R2
unknown gap                         ....................

20_terminology.txt

# Words like "fragment size" or "insert size" are confusing. Here's what they usually mean.

PE reads      R1--------->                    <---------R2
fragment     ~~~========================================~~~
insert          ========================================
inner mate                ....................

30_overlapping.txt

# Sometimes, R1 & R2 reads will overlap

fragment          ~~~========================================~~~
insert               ========================================
R1                   ------------------------->                    
R2                                   <-----------------------
overlap                              ::::::::::
stitched SE read     --------------------------------------->

40_adapters.txt

# On very tiny fragments, we see adapters on the ends of each of our reads

tiny fragment       ~~~~========================~~~~
insert                  ========================
R1                      -------------------------->                    
R2                   <--------------------------
read-through         !!!                        !!!