Assume that the sample DNA sequence has no reverse mutation, the mapping result expected should be like this:

                    5'                                                                      
template to seq     X1X2X3X4..............................................................................Xn-3Xn-2Xn-1Xn   
  (for example)     |------------------------------------------------------------------------------------------------->|
      reads         5'---------->3'                                                                      3'<----------5'    
                    X1X2X3X4                                                                          X'n-3X'n-2X'n-1X'n

So assuming /1 corresponds to 5->3 of the template, /2 correspond to the 5->3 of the complementary strand of the template:

The output reads of the strand coming from the ref strand should be:

/1(template 5->3)   X1X2X3X4...
/2(other end of the template, reversed complementary, 5->3)  X'nX'n-1X'n-2X'n-3

Similarly, the output reads of strand coming from the alt strand should be:

/1(template 5->3)    X'nX'n-1X'n-2X'n-3
/2(other end of the template, reversed complementary, 5->3)       X1X2X3X4...

Right?

No matter which strand the template comes from and the 1/2 labeling definition, the output reads always start with 5', and the 5' are always at the outsider of the template, which means reads are always like this:

template: |------------------------------------------------------------------------------------------------->|
reads   : 5'---------->3'                                                                      3'<----------5'

instead of this:

template: |------------------------------------------------------------------------------------------------->|
reads   : 3'<----------5'                                                                       5'--------->3'

right?

Thank you!