Mutations play a pivotal role as a driver of genome evolution in organisms across the tree of life. However, site-specific mutation rates appear to have a non-uniform mutation rate and vary across the genome. Currently, site-specific variation has not been well characterized or analyzed using a uniform treatment. To address the lack of uniform analysis and provide an open-source, non-proprietary means of in-depth analysis, we developed the Context Dependent Mutation Analysis Pipeline (CDMAP for short). CDMAP is a novel pipeline that provides an automated, end-to-end, reproducible pipeline that provides in-depth analysis of genome-wide and replichore specific mutation rates and nucleotide triplet usage in bacterial prokaryotes. Additionally, we utilize the CDMAP pipeline to investigate patterns influencing genomic nucleotide triplets and synonymous codon usage through the lens of genomic GC content and various spatiotemporal factors.