Ambiguous symbols

The symbols page lists all symbols that the underlying sequence files in .FASTA format can contain. The ambiguous symbols arise from imperfect reads in the sequencer.

While one mostly queries for the symbols A, C, G, T and - to look for specific features and mutations of a sequence, or N for quality control of the underlying data, the ambiguous symbols R through V are often too cumbersome to consider in analyses.

LAPIS supports the flexible consideration of these ambiguous symbols through an extension of the boolean logic syntax in the variant queries.

Here we introduce a new expression MAYBE to consider sequences that have an ambiguous code which maybe matches the queried value.

Example

Consider the following sequences:

12345
AAACG
AARCG
AANCG
AAGCG
AAACG

A filter for the mutation 3G returns only the sequence AAGCG, as it is the only sequence with the symbol G at position 3. The filter MAYBE(3G) however also considers that the sequences AARCG and AANCG may have the symbol G at position 3, because the symbols R and N can represent Guanine.