Hello,

I'm quite new at using Samtools and figuring my way around it. I am looking for SNPs for some disorders, and I got the following output:

2   #position   G   8   .a,...,.    ]]]]]]]]    FFFFFFFF

I understood that the 5th column tells me whether . or , means a base matching to the reference base on the forward or reverse strand. Does this mean all the reads having stops (.) are G, and hence all commas(,) are C? Is there a way to see the actual alleles obtained in these reads?

Thanks a lot!!