Base calling .—Computational process in massively parallel sequencing for translating raw electrical 24


signals to nucleotide sequence (8)


Base composition .—Percentage of GC base pairs in the genome

Biothreat agent (biological agent) .—Any microorganism (including, but not limited to, bacteria, viruses, 27

fungi, or protozoa), or infectious substance, or any naturally occurring, bioengineered, or synthesized 28

component of any such microorganism or infectious substance, capable of causing: (1) Death, disease, 29

or other biological malfunction in a human, an animal, a plant, or another living organism; (2) 30

Deterioration of food, water, equipment, supplies, or material of any kind; or (3) Deleterious alteration 31

of the environment: biological, virological, or toxic threat select agents (BSAT) are identified in a list provided 32

by the US federal select agent program ( (9) 33

Breadth of coverage. —The percentage of genome bases sequenced at a given coverage (sequencing 34


depth) (10)

Cluster density. —Number of templates present on a NGS sequencing cell 36

Context .—Circumstance, purpose, and perspective under which an object is defined or used 37

Contig.— A contiguous stretch of DNA sequence that results from the assembly of smaller, overlapping 38


DNA sequence reads

Coverage .—Number of times that a given base position is read in a sequencing run (11, 12) 40

Detection .—Recognition of the presence of the target nucleic acid 41

Extensible markup language (XML) .—Markup language that encodes information in a way that is 42


machine-processable as well as human-readable

FAST5 format .—Standard sequencing output for Oxford Nanopore sequencers 44

FASTQ format .—Text-based format for storing both a biological sequence (usually nucleotide sequence) 45

and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a 46


single ASCII character for brevity.

AOAC Draft Standard – Version 09282022; Public Comment Revisions


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