What categories of genomic alterations are identified by the method of genomic profiling you are familiar with? Are any critical genomic alterations not identified by NGS?

What categories of genomic alterations are identified by the method of genomic profiling you are familiar with? Do they include all classes of alterations, i.e. base substitutions, insertions/deletions, copy number alterations and rearrangements? Are any critical genomic alterations not identified by NGS?