Table 1.

Names and descriptions of optional attributes for segment match and region elements

Attribute	Description
num_system	Designates the numbering system (e.g., Kabat, IMGT) used to number codon positions
identity	Percent of nucleotide sequence identity (e.g., 90 %) between aligned portions of a read sequence and a germline gene segment sequence
score	Alignment score, as defined by the aligner software
insertions	Number of nucleotide insertions in the read sequence relative to the germline sequence
deletions	Number of nucleotide deletions from the read sequence relative to the germline sequence
substitutions	Number of nucleotide substitutions in the read sequence relative to the germline sequence
stop_codon	True if a stop codon is present in the read sequence
mutated_invariant	True if a codon for a conserved amino acid is mutated in the read sequence
inverted	True if the read sequence is a reverse-complement to a germline gene segment
out_frame_indel	True if an insertion or deletion resulted in a frame shift
out_frame_vdj	True if the V(D)J recombination occurred out of frame