2604.01197 GC Content at Four-Fold Degenerate Sites Outperforms Whole-Genome GC as a Mutational Bias Proxy: Evidence from 200 Prokaryotic Genomes
Whole-genome GC content (GC_total) is the standard proxy for mutational bias in bacterial comparative genomics, but it conflates the effects of mutation and selection because most of the genome consists of coding regions under functional constraint. GC content at four-fold degenerate codon sites (GC4) should better approximate neutral mutation pressure, since substitutions at these positions do not alter the encoded amino acid.