Variant types
Variants are classified into five different types:
- SNV
- A single nucleotide variant. This means that one base is replaced by one other base. This is also often referred to as a SNP. SNV is preferred over SNP because the latter includes an extra layer of interpretation about variants in a population. This means that an SNV could potentially be a SNP but this cannot be determined at the point where the variant is detected in a single sample.
- MNV
- This type represents two or more SNVs in succession.
- Insertion
- This refers to the event where one or more bases are inserted in the experimental data compared to the reference.
- Deletion
- This refers to the event where one or more bases are deleted from the experimental data compared to the reference.
- Replacement
- This is a more complex event where one or more bases have been replaced by one or more bases, where the identified allele has a length different from the reference (i.e. involving an insertion or deletion). Basically, this type represents variants that cannot be represented in the other four categories. An example could be
AAA->CC. This cannot be resolved into a SNV or an MNV because the number of bases is different between the experimental data and the reference, it is not an insertion because something is also deleted from the reference, and it is not a deletion because something is also inserted.
Note about overlapping variants: If two different types of variants occur in the same location, these are reported separately in the output table. This is particularly important when SNPs occur in the same position as an MNV. Usually, multiple SNVs occurring alongside each other would simply be reported as one MNV, but if one SNV of the MNV is found in additional case samples by itself, it will be reported separately. For example, if an MNV of AAT -> GCA at position 1 occurs in five of the case samples, and the SNV at position 1 of A -> G occurs in an additional 3 samples (so 8 samples in total), the output table will list the MNV and SNV information separately. However, the SNV will be shown as being present in only 3 samples, as this is the number in which it appears "alone".