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AAshort for amino acid
aligneda 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.
Mutationa divergence from the reference genome (see mutation-filters).
OrganismThe organism that the genomic data was extracted from. Each LAPIS instance serves data for a single organism.
QCquality 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.
SegmentThe genome of an organism may consist of multiple nucleotide sequence pieces. We call those pieces “segments”.
VariantWe 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.