When comparing two genomes (strings), the differences can occur in 3 ways: substitution, insertion and deletion of one or more characters.
Single-nucleotide polymorphisms (SNPs)
refers to the difference where only one character (one nucleotide letter) is substituted by another in the genome.
Small insertions/deletions (INDELs)
refers to the difference where one or more characters are inserted or deleted in the genome.
INDELs happen less frequently than SNPs and are harder to call.
De Novo mutations (DNM)
occur when sperms/eggs were produced. These are new mutations seen in the new generation but not in parents.
DNMs occur ~30-40 per haploid genome (in one sperm or egg), meaning each offspring carries ~70 to 80 DNMs. Calculation: human mutation rate 1.1 x 10^-8 bp per generation, times 3.1 billion bp, leads to ~34bp per gamete cell.