Name	Type	Attributes	Definition
sequence_id	string	required, identifier, nullable	"Unique query sequence identifier for the Rearrangement. Most often this will be the input sequence header or a substring thereof, but may also be a custom identifier defined by the tool in cases where query sequences have been combined in some fashion prior to alignment. When downloaded from an AIRR Data Commons repository, this will usually be a universally unique record locator for linking with other objects in the AIRR Data Model.
"
sequence	string	required, nullable	"The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment.
"
quality	string	optional, nullable	"The Sanger/Phred quality scores for assessment of sequence quality. Phred quality scores from 0 to 93 are encoded using ASCII 33 to 126 (Used by Illumina from v1.8.)
"
sequence_aa	string	optional, nullable	"Amino acid translation of the query nucleotide sequence.
"
rev_comp	boolean	required, nullable	"True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'.
"
productive	boolean	required, nullable	"True if the V(D)J sequence is predicted to be productive.
"
vj_in_frame	boolean	optional, nullable	True if the V and J gene alignments are in-frame.
stop_codon	boolean	optional, nullable	True if the aligned sequence contains a stop codon.
complete_vdj	boolean	optional, nullable	"True if the sequence alignment spans the entire V(D)J region. Meaning, sequence_alignment includes both the first V gene codon that encodes the mature polypeptide chain (i.e., after the leader sequence) and the last complete codon of the J gene (i.e., before the J-C splice site). This does not require an absence of deletions within the internal FWR and CDR regions of the alignment.
"
locus	string	optional, nullable	"Gene locus (chain type). Note that this field uses a controlled vocabulary that is meant to provide a generic classification of the locus, not necessarily the correct designation according to a specific nomenclature.
"
v_call	string	required, nullable	"V gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHV4-59*01 if using IMGT/GENE-DB).
"
d_call	string	required, nullable	"First or only D gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHD3-10*01 if using IMGT/GENE-DB).
"
d2_call	string	optional, nullable	"Second D gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHD3-10*01 if using IMGT/GENE-DB).
"
j_call	string	required, nullable	"J gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHJ4*02 if using IMGT/GENE-DB).
"
c_call	string	optional, nullable	"Constant region gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHG1*01 if using IMGT/GENE-DB).
"
sequence_alignment	string	required, nullable	"Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement.
"
quality_alignment	string	optional, nullable	"Sanger/Phred quality scores for assessment of sequence_alignment quality. Phred quality scores from 0 to 93 are encoded using ASCII 33 to 126 (Used by Illumina from v1.8.)
"
sequence_alignment_aa	string	optional, nullable	"Amino acid translation of the aligned query sequence.
"
germline_alignment	string	required, nullable	"Assembled, aligned, full-length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any).
"
germline_alignment_aa	string	optional, nullable	"Amino acid translation of the assembled germline sequence.
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junction	string	required, nullable	"Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons.
"
junction_aa	string	required, nullable	"Amino acid translation of the junction.
"
np1	string	optional, nullable	"Nucleotide sequence of the combined N/P region between the V gene and first D gene alignment or between the V gene and J gene alignments.
"
np1_aa	string	optional, nullable	"Amino acid translation of the np1 field.
"
np2	string	optional, nullable	"Nucleotide sequence of the combined N/P region between either the first D gene and J gene alignments or the first D gene and second D gene alignments.
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np2_aa	string	optional, nullable	"Amino acid translation of the np2 field.
"
np3	string	optional, nullable	"Nucleotide sequence of the combined N/P region between the second D gene and J gene alignments.
"
np3_aa	string	optional, nullable	"Amino acid translation of the np3 field.
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cdr1	string	optional, nullable	"Nucleotide sequence of the aligned CDR1 region.
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cdr1_aa	string	optional, nullable	"Amino acid translation of the cdr1 field.
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cdr2	string	optional, nullable	"Nucleotide sequence of the aligned CDR2 region.
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cdr2_aa	string	optional, nullable	"Amino acid translation of the cdr2 field.
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cdr3	string	optional, nullable	"Nucleotide sequence of the aligned CDR3 region.
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cdr3_aa	string	optional, nullable	"Amino acid translation of the cdr3 field.
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fwr1	string	optional, nullable	"Nucleotide sequence of the aligned FWR1 region.
"
fwr1_aa	string	optional, nullable	"Amino acid translation of the fwr1 field.
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fwr2	string	optional, nullable	"Nucleotide sequence of the aligned FWR2 region.
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fwr2_aa	string	optional, nullable	"Amino acid translation of the fwr2 field.
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fwr3	string	optional, nullable	"Nucleotide sequence of the aligned FWR3 region.
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fwr3_aa	string	optional, nullable	"Amino acid translation of the fwr3 field.
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fwr4	string	optional, nullable	"Nucleotide sequence of the aligned FWR4 region.
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fwr4_aa	string	optional, nullable	"Amino acid translation of the fwr4 field.
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v_score	number	optional, nullable	Alignment score for the V gene.
v_identity	number	optional, nullable	Fractional identity for the V gene alignment.
v_support	number	optional, nullable	"V gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the V gene assignment as defined by the alignment tool.
"
v_cigar	string	required, nullable	CIGAR string for the V gene alignment.
d_score	number	optional, nullable	Alignment score for the first or only D gene alignment.
d_identity	number	optional, nullable	Fractional identity for the first or only D gene alignment.
d_support	number	optional, nullable	"D gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the first or only D gene as defined by the alignment tool.
"
d_cigar	string	required, nullable	CIGAR string for the first or only D gene alignment.
d2_score	number	optional, nullable	Alignment score for the second D gene alignment.
d2_identity	number	optional, nullable	Fractional identity for the second D gene alignment.
d2_support	number	optional, nullable	"D gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the second D gene as defined by the alignment tool.
"
d2_cigar	string	optional, nullable	CIGAR string for the second D gene alignment.
j_score	number	optional, nullable	Alignment score for the J gene alignment.
j_identity	number	optional, nullable	Fractional identity for the J gene alignment.
j_support	number	optional, nullable	"J gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the J gene assignment as defined by the alignment tool.
"
j_cigar	string	required, nullable	CIGAR string for the J gene alignment.
c_score	number	optional, nullable	Alignment score for the C gene alignment.
c_identity	number	optional, nullable	Fractional identity for the C gene alignment.
c_support	number	optional, nullable	"C gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the C gene assignment as defined by the alignment tool.
"
c_cigar	string	optional, nullable	CIGAR string for the C gene alignment.
v_sequence_start	integer	optional, nullable	"Start position of the V gene in the query sequence (1-based closed interval).
"
v_sequence_end	integer	optional, nullable	"End position of the V gene in the query sequence (1-based closed interval).
"
v_germline_start	integer	optional, nullable	"Alignment start position in the V gene reference sequence (1-based closed interval).
"
v_germline_end	integer	optional, nullable	"Alignment end position in the V gene reference sequence (1-based closed interval).
"
v_alignment_start	integer	optional, nullable	"Start position of the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
v_alignment_end	integer	optional, nullable	"End position of the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
d_sequence_start	integer	optional, nullable	"Start position of the first or only D gene in the query sequence. (1-based closed interval).
"
d_sequence_end	integer	optional, nullable	"End position of the first or only D gene in the query sequence. (1-based closed interval).
"
d_germline_start	integer	optional, nullable	"Alignment start position in the D gene reference sequence for the first or only D gene (1-based closed interval).
"
d_germline_end	integer	optional, nullable	"Alignment end position in the D gene reference sequence for the first or only D gene (1-based closed interval).
"
d_alignment_start	integer	optional, nullable	"Start position of the first or only D gene in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
d_alignment_end	integer	optional, nullable	"End position of the first or only D gene in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
d2_sequence_start	integer	optional, nullable	"Start position of the second D gene in the query sequence (1-based closed interval).
"
d2_sequence_end	integer	optional, nullable	"End position of the second D gene in the query sequence (1-based closed interval).
"
d2_germline_start	integer	optional, nullable	"Alignment start position in the second D gene reference sequence (1-based closed interval).
"
d2_germline_end	integer	optional, nullable	"Alignment end position in the second D gene reference sequence (1-based closed interval).
"
d2_alignment_start	integer	optional, nullable	"Start position of the second D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
d2_alignment_end	integer	optional, nullable	"End position of the second D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
j_sequence_start	integer	optional, nullable	"Start position of the J gene in the query sequence (1-based closed interval).
"
j_sequence_end	integer	optional, nullable	"End position of the J gene in the query sequence (1-based closed interval).
"
j_germline_start	integer	optional, nullable	"Alignment start position in the J gene reference sequence (1-based closed interval).
"
j_germline_end	integer	optional, nullable	"Alignment end position in the J gene reference sequence (1-based closed interval).
"
j_alignment_start	integer	optional, nullable	"Start position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
j_alignment_end	integer	optional, nullable	"End position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
c_sequence_start	integer	optional, nullable	"Start position of the C gene in the query sequence (1-based closed interval).
"
c_sequence_end	integer	optional, nullable	"End position of the C gene in the query sequence (1-based closed interval).
"
c_germline_start	integer	optional, nullable	"Alignment start position in the C gene reference sequence (1-based closed interval).
"
c_germline_end	integer	optional, nullable	"Alignment end position in the C gene reference sequence (1-based closed interval).
"
c_alignment_start	integer	optional, nullable	"Start position of the C gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
c_alignment_end	integer	optional, nullable	"End position of the C gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
"
cdr1_start	integer	optional, nullable	CDR1 start position in the query sequence (1-based closed interval).
cdr1_end	integer	optional, nullable	CDR1 end position in the query sequence (1-based closed interval).
cdr2_start	integer	optional, nullable	CDR2 start position in the query sequence (1-based closed interval).
cdr2_end	integer	optional, nullable	CDR2 end position in the query sequence (1-based closed interval).
cdr3_start	integer	optional, nullable	CDR3 start position in the query sequence (1-based closed interval).
cdr3_end	integer	optional, nullable	CDR3 end position in the query sequence (1-based closed interval).
fwr1_start	integer	optional, nullable	FWR1 start position in the query sequence (1-based closed interval).
fwr1_end	integer	optional, nullable	FWR1 end position in the query sequence (1-based closed interval).
fwr2_start	integer	optional, nullable	FWR2 start position in the query sequence (1-based closed interval).
fwr2_end	integer	optional, nullable	FWR2 end position in the query sequence (1-based closed interval).
fwr3_start	integer	optional, nullable	FWR3 start position in the query sequence (1-based closed interval).
fwr3_end	integer	optional, nullable	FWR3 end position in the query sequence (1-based closed interval).
fwr4_start	integer	optional, nullable	FWR4 start position in the query sequence (1-based closed interval).
fwr4_end	integer	optional, nullable	FWR4 end position in the query sequence (1-based closed interval).
v_sequence_alignment	string	optional, nullable	"Aligned portion of query sequence assigned to the V gene, including any indel corrections or numbering spacers.
"
v_sequence_alignment_aa	string	optional, nullable	"Amino acid translation of the v_sequence_alignment field.
"
d_sequence_alignment	string	optional, nullable	"Aligned portion of query sequence assigned to the first or only D gene, including any indel corrections or numbering spacers.
"
d_sequence_alignment_aa	string	optional, nullable	"Amino acid translation of the d_sequence_alignment field.
"
d2_sequence_alignment	string	optional, nullable	"Aligned portion of query sequence assigned to the second D gene, including any indel corrections or numbering spacers.
"
d2_sequence_alignment_aa	string	optional, nullable	"Amino acid translation of the d2_sequence_alignment field.
"
j_sequence_alignment	string	optional, nullable	"Aligned portion of query sequence assigned to the J gene, including any indel corrections or numbering spacers.
"
j_sequence_alignment_aa	string	optional, nullable	"Amino acid translation of the j_sequence_alignment field.
"
c_sequence_alignment	string	optional, nullable	"Aligned portion of query sequence assigned to the constant region, including any indel corrections or numbering spacers.
"
c_sequence_alignment_aa	string	optional, nullable	"Amino acid translation of the c_sequence_alignment field.
"
v_germline_alignment	string	optional, nullable	"Aligned V gene germline sequence spanning the same region as the v_sequence_alignment field and including the same set of corrections and spacers (if any).
"
v_germline_alignment_aa	string	optional, nullable	"Amino acid translation of the v_germline_alignment field.
"
d_germline_alignment	string	optional, nullable	"Aligned D gene germline sequence spanning the same region as the d_sequence_alignment field and including the same set of corrections and spacers (if any).
"
d_germline_alignment_aa	string	optional, nullable	"Amino acid translation of the d_germline_alignment field.
"
d2_germline_alignment	string	optional, nullable	"Aligned D gene germline sequence spanning the same region as the d2_sequence_alignment field and including the same set of corrections and spacers (if any).
"
d2_germline_alignment_aa	string	optional, nullable	"Amino acid translation of the d2_germline_alignment field.
"
j_germline_alignment	string	optional, nullable	"Aligned J gene germline sequence spanning the same region as the j_sequence_alignment field and including the same set of corrections and spacers (if any).
"
j_germline_alignment_aa	string	optional, nullable	"Amino acid translation of the j_germline_alignment field.
"
c_germline_alignment	string	optional, nullable	"Aligned constant region germline sequence spanning the same region as the c_sequence_alignment field and including the same set of corrections and spacers (if any).
"
c_germline_alignment_aa	string	optional, nullable	"Amino acid translation of the c_germline_aligment field.
"
junction_length	integer	optional, nullable	Number of nucleotides in the junction sequence.
junction_aa_length	integer	optional, nullable	Number of amino acids in the junction sequence.
np1_length	integer	optional, nullable	"Number of nucleotides between the V gene and first D gene alignments or between the V gene and J gene alignments.
"
np2_length	integer	optional, nullable	"Number of nucleotides between either the first D gene and J gene alignments or the first D gene and second D gene alignments.
"
np3_length	integer	optional, nullable	"Number of nucleotides between the second D gene and J gene alignments.
"
n1_length	integer	optional, nullable	Number of untemplated nucleotides 5' of the first or only D gene alignment.
n2_length	integer	optional, nullable	Number of untemplated nucleotides 3' of the first or only D gene alignment.
n3_length	integer	optional, nullable	Number of untemplated nucleotides 3' of the second D gene alignment.
p3v_length	integer	optional, nullable	Number of palindromic nucleotides 3' of the V gene alignment.
p5d_length	integer	optional, nullable	Number of palindromic nucleotides 5' of the first or only D gene alignment.
p3d_length	integer	optional, nullable	Number of palindromic nucleotides 3' of the first or only D gene alignment.
p5d2_length	integer	optional, nullable	Number of palindromic nucleotides 5' of the second D gene alignment.
p3d2_length	integer	optional, nullable	Number of palindromic nucleotides 3' of the second D gene alignment.
p5j_length	integer	optional, nullable	Number of palindromic nucleotides 5' of the J gene alignment.
v_frameshift	boolean	optional, nullable	"True if the V gene in the query nucleotide sequence contains a translational frameshift relative to the frame of the V gene reference sequence.
"
j_frameshift	boolean	optional, nullable	"True if the J gene in the query nucleotide sequence contains a translational frameshift relative to the frame of the J gene reference sequence.
"
d_frame	integer	optional, nullable	"Numerical reading frame (1, 2, 3) of the first or only D gene in the query nucleotide sequence, where frame 1 is relative to the first codon of D gene reference sequence.
"
d2_frame	integer	optional, nullable	"Numerical reading frame (1, 2, 3) of the second D gene in the query nucleotide sequence, where frame 1 is relative to the first codon of D gene reference sequence.
"
consensus_count	integer	optional, nullable	"Number of reads contributing to the UMI consensus or contig assembly for this sequence. For example, the sum of the number of reads for all UMIs that contribute to the query sequence.
"
duplicate_count	integer	optional, nullable	"Copy number or number of duplicate observations for the query sequence. For example, the number of identical reads observed for this sequence.
"
umi_count	integer	optional, nullable	"Number of distinct UMIs represented by this sequence. For example, the total number of UMIs that contribute to the contig assembly for the query sequence.
"
cell_id	string	optional, identifier, nullable	"Identifier defining the cell of origin for the query sequence.
"
clone_id	string	optional, identifier, nullable	Clonal cluster assignment for the query sequence.
repertoire_id	string	optional, identifier, nullable	Identifier to the associated repertoire in study metadata.
sample_processing_id	string	optional, identifier, nullable	"Identifier to the sample processing object in the repertoire metadata for this rearrangement. If the repertoire has a single sample then this field may be empty or missing. If the repertoire has multiple samples then this field may be empty or missing if the sample cannot be differentiated or the relationship is not maintained by the data processing.
"
data_processing_id	string	optional, identifier, nullable	"Identifier to the data processing object in the repertoire metadata for this rearrangement. If this field is empty than the primary data processing object is assumed.
"
rearrangement_id	string	DEPRECATED	"Identifier for the Rearrangement object. May be identical to sequence_id, but will usually be a universally unique record locator for database applications.
"
rearrangement_set_id	string	DEPRECATED	"Identifier for grouping Rearrangement objects.
"
germline_database	string	DEPRECATED	Source of germline V(D)J genes with version number or date accessed.