Table 1 Names and descriptions of optional attributes for segment match and region elements

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