I have identified nonsynonymous mutation occurs on the contig position 1000 substitution by G/A through variant effect predictor. I got the transcript id & protein id and sequences of them. Now I am trying to know whether my SNP is neutral or deleterious, I am trying to use polyphen2, but it ask for the position in the amino acid sequence. How to correctly specify the substitution position in protein sequence which obtained from contig position.?