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 mater 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!