| AA |
short for amino acid |
| aligned |
a nucleotide sequence is aligned, if it is arranged such that it has many similarities to a given reference genome. The aligned sequence has the same length as the reference genome. Gaps are marked in the aligned sequence. Insertions are stored separately. |
| Mutation |
a divergence from the reference genome (see mutation-filters). |
| Organism |
The organism that the genomic data was extracted from. Each LAPIS instance serves data for a single organism. |
| QC |
quality control; in our case, it usually refers to the quality checks and metrics of the sequences, targeting how well the nucleotide sequence was determined from the probe. |
| Segment |
The genome of an organism may consist of multiple nucleotide sequence pieces. We call those pieces “segments”. |
| Variant |
We follow a very open definition of variants. Every subset of sequences is considered a variant. A variant is specified by lineage/clade names and mutations. A variant does not need to be monophyletic. |