[Brian Bushnell]

Is that the distance M=N=I=D=S=1??
any response Brian?

The match strings are like expanded cigar strings, with one character per operation. So a read with 3 matches, then 2 substitutions, then 4 matches would have this match string:

mmmSSmmmm

In other words, every letter corresponds to 1 operation (basically 1 base). Does that answer your question?

[mido1951]

for me, I want to express the error rate in the equation.
From what I understood the error rate is equal: error rate = (S+I+D+N)/(M+S+I+D+N)
am i right?
then I want to see the distance used for each operation of M,S,I,D,N.
and from what you told me each operation takes one unit(operation) = 1.
am i right for this?
thanks

[Brian Bushnell]

Yes, that is correct.