Maq filtered output.

[tachion]

Hello,

I am trying to find what SNPs the MAQ finds with respect to its reported location and reference base in its filtered output. Is this what the consensus column is? If so, there are sometimes letters such as "S" . I understand that these represent genotypes. If the consensus column is what I am looking for, How do I account the genotype being a SNP?

Thanks,
Willard