I am working on non-model organism. I have called SNPs by read mapping illumina reads to reference genome(assembled contigs/scaffolds). I have VCF file with SNP predicted for each contig/scaffold. Recently Ensembl released non-chromosomal genome assembly and also have GTF file(gene prediction based on Ensembl annotation). Now I am trying to find out synonymous and nonsynonymous mutation rate. I find tools that only available for chromosomal level, Is there any script or tool available already for contig level?.