Table 2.

GLUE samReporter commands.

Command	Description
nucleotide	Generate a table of nucleotide frequencies within a specific genome region.
depth	Generate a table of read depths within a specific genome region.
nucleotide-consensus	Generate a FASTA consensus file, optionally using ambiguity codes.
amino-acid	Generate a table of amino acid residue frequencies within a specific protein-coding region.
codon-triplets	Generate a table of codon frequencies within a specific protein-coding region.
variation scan	Scan for the presence or absence of GLUE Variations within reads.
export nucleotide-alignment	Export a specific part of the SAM alignment as a FASTA file.