How can I calculate the silent mutation for each position in codon? I am trying to find the number of silent mutations in for each position in codon.

In the homework, I am asked:


  For the codons and for each position, count the number of silent mutation. There are 64 codons, for each position there are 3 mutations leading to a change at the DNA level. There are thus 192 possible mutations for each of the three positions of the codons. For each position, print the number of silent mutations.


I understand stand silent mutation is the mutation that doesn't lead to amino acid change. For example, GCC can become GCT but it is still Thr

I am not sure what does "calculating silent mutation for each position" mean? I mean it is easy to find silent mutation for each codon like the example I gave above, but couldn't really understand how to calculate the silent mutation for each position.

Should I change letters (nucleotides) one by one and see if it causing a silent mutation?
Calculate in this context would just mean determine. You don't actually have to change every base to determine whether a change is silent. Instead, try building a hash table of amino acids to codons, which you can then quickly iterate over to find all silent changes.

BTW, try to avoid loaded terms like "mutation", even if your professor incorrectly used it. Terming things like this as "silent polymorphism" or "silent change" or something along those lines is preferable.