Mutation is the fuel of evolution, and is of fundamental importance in evolutionary biology. A usual and efficient way to estimate the properties of spontaneous mutation divorced from the influence of natural selection is by means of mutation accumulation (MA) experiments, in which the efficacy of selection is minimized. However, MA experiments potentially come with their own biases. Previous studies have consistently shown a discrepancy between the mutation spectrum observed in MA lines and the site frequency spectrum (SFS) of wild isolates. By applying MA experiments and whole genome sequencing to three strains of C. elegans, (N2, PB306, and an N2-derived strain carrying a defective allele at the
mev-1 gene), we investigated the property of spontaneous mutations in different part of the genome. We find that the mutational properties of mononucleotide repeats differ in both rate and spectrum from non-mononucleotide sequences, both for base-substitutions and insertion/deletion (indel) mutations. Comparison of the MA spectrum to that of segregating "private" alleles (which have presumably arisen recently as new mutations) reveals that the spectra at non-mononucleotides are similar between MA lines and wild isolates, whereas the mononucleotide spectra are very different, both for base-substitutions and indels. In addition, we compared the mutational properties of highly divergent regions of the C. elegans genome to those of weakly diverged regions. Our preliminary analysis suggests that the mutation rate is slightly higher in divergent regions, but the difference in mutation rate is not nearly large enough to explain the difference in nucleotide diversity.