Mismatch position in reads

[lmf_bill]

Hi,
when I using mapreads for SOLiD data mapping, it only gives the number of mismatch. How can i get the positions(relative to read) of mismatch? anyone can help me? thanks!

[westerman]

I believe that the pipeline will not give you the position with just mapreads. If you run the SNP calling part of the pipeline it will generate GFF-format files with the position information.