Class: Rearrangement

name: Rearrangement
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- sequence_id
- sequence
- quality
- sequence_aa
- rev_comp
- productive
- vj_in_frame
- stop_codon
- complete_vdj
- locus
- v_call
- d_call
- d2_call
- j_call
- c_call
- sequence_alignment
- quality_alignment
- sequence_alignment_aa
- germline_alignment
- germline_alignment_aa
- junction
- junction_aa
- np1
- np1_aa
- np2
- np2_aa
- np3
- np3_aa
- cdr1
- cdr1_aa
- cdr2
- cdr2_aa
- cdr3
- cdr3_aa
- fwr1
- fwr1_aa
- fwr2
- fwr2_aa
- fwr3
- fwr3_aa
- fwr4
- fwr4_aa
- v_score
- v_identity
- v_support
- v_cigar
- d_score
- d_identity
- d_support
- d_cigar
- d2_score
- d2_identity
- d2_support
- d2_cigar
- j_score
- j_identity
- j_support
- j_cigar
- c_score
- c_identity
- c_support
- c_cigar
- v_sequence_start
- v_sequence_end
- v_germline_start
- v_germline_end
- v_alignment_start
- v_alignment_end
- d_sequence_start
- d_sequence_end
- d_germline_start
- d_germline_end
- d_alignment_start
- d_alignment_end
- d2_sequence_start
- d2_sequence_end
- d2_germline_start
- d2_germline_end
- d2_alignment_start
- d2_alignment_end
- j_sequence_start
- j_sequence_end
- j_germline_start
- j_germline_end
- j_alignment_start
- j_alignment_end
- c_sequence_start
- c_sequence_end
- c_germline_start
- c_germline_end
- c_alignment_start
- c_alignment_end
- cdr1_start
- cdr1_end
- cdr2_start
- cdr2_end
- cdr3_start
- cdr3_end
- fwr1_start
- fwr1_end
- fwr2_start
- fwr2_end
- fwr3_start
- fwr3_end
- fwr4_start
- fwr4_end
- v_sequence_alignment
- v_sequence_alignment_aa
- d_sequence_alignment
- d_sequence_alignment_aa
- d2_sequence_alignment
- d2_sequence_alignment_aa
- j_sequence_alignment
- j_sequence_alignment_aa
- c_sequence_alignment
- c_sequence_alignment_aa
- v_germline_alignment
- v_germline_alignment_aa
- d_germline_alignment
- d_germline_alignment_aa
- d2_germline_alignment
- d2_germline_alignment_aa
- j_germline_alignment
- j_germline_alignment_aa
- c_germline_alignment
- c_germline_alignment_aa
- junction_length
- junction_aa_length
- np1_length
- np2_length
- np3_length
- n1_length
- n2_length
- n3_length
- p3v_length
- p5d_length
- p3d_length
- p5d2_length
- p3d2_length
- p5j_length
- v_frameshift
- j_frameshift
- d_frame
- d2_frame
- consensus_count
- duplicate_count
- umi_count
- cell_id
- clone_id
- repertoire_id
- sample_processing_id
- data_processing_id

name: Rearrangement
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  sequence_id:
    name: sequence_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_id
    owner: Rearrangement
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - Alignment
    - Rearrangement
    - Node
    range: string
  sequence:
    name: sequence
    description: Nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence
    owner: Rearrangement
    domain_of:
    - Chain
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - UndocumentedAllele
    - Rearrangement
    range: string
  quality:
    name: quality
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.)
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: quality
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  sequence_aa:
    name: sequence_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the query nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_aa
    owner: Rearrangement
    domain_of:
    - Chain
    - PeptidicEpitope
    - Rearrangement
    range: string
  rev_comp:
    name: rev_comp
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: rev_comp
    owner: Rearrangement
    domain_of:
    - Alignment
    - Rearrangement
    range: boolean
  productive:
    name: productive
    annotations:
      nullable:
        tag: nullable
        value: true
    description: True if the V(D)J sequence is predicted to be productive.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: productive
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: boolean
  vj_in_frame:
    name: vj_in_frame
    annotations:
      nullable:
        tag: nullable
        value: true
    description: True if the V and J gene alignments are in-frame.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: vj_in_frame
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: boolean
  stop_codon:
    name: stop_codon
    annotations:
      nullable:
        tag: nullable
        value: true
    description: True if the aligned sequence contains a stop codon.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: stop_codon
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: boolean
  complete_vdj:
    name: complete_vdj
    description: Complete VDJ flag.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: complete_vdj
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    range: boolean
  locus:
    name: locus
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: locus
    owner: Rearrangement
    domain_of:
    - AlleleDescription
    - GermlineSet
    - Genotype
    - Rearrangement
    range: LocusEnum
  v_call:
    name: v_call
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_call
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  d_call:
    name: d_call
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_call
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  d2_call:
    name: d2_call
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_call
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  j_call:
    name: j_call
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_call
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    range: string
  c_call:
    name: c_call
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_call
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    range: string
  sequence_alignment:
    name: sequence_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Node
    range: string
  quality_alignment:
    name: quality_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.)
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: quality_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  sequence_alignment_aa:
    name: sequence_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the aligned query sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  germline_alignment:
    name: germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: string
  germline_alignment_aa:
    name: germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: germline_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: string
  junction:
    name: junction
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    - Node
    range: string
  junction_aa:
    name: junction_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the junction.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_aa
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    - Clone
    - Node
    range: string
  np1:
    name: np1
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np1
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  np1_aa:
    name: np1_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the np1 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np1_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  np2:
    name: np2
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np2
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  np2_aa:
    name: np2_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the np2 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np2_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  np3:
    name: np3
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the combined N/P region between the second
      D gene and J gene alignments.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np3
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  np3_aa:
    name: np3_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the np3 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np3_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  cdr1:
    name: cdr1
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned CDR1 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  cdr1_aa:
    name: cdr1_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the cdr1 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1_aa
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    range: string
  cdr2:
    name: cdr2
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned CDR2 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  cdr2_aa:
    name: cdr2_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the cdr2 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2_aa
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    range: string
  cdr3:
    name: cdr3
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned CDR3 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  cdr3_aa:
    name: cdr3_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the cdr3 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3_aa
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    range: string
  fwr1:
    name: fwr1
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned FWR1 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr1
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr1_aa:
    name: fwr1_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the fwr1 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr1_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr2:
    name: fwr2
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned FWR2 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr2
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr2_aa:
    name: fwr2_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the fwr2 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr2_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr3:
    name: fwr3
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned FWR3 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr3
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr3_aa:
    name: fwr3_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the fwr3 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr3_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr4:
    name: fwr4
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Nucleotide sequence of the aligned FWR4 region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr4
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  fwr4_aa:
    name: fwr4_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the fwr4 field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr4_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  v_score:
    name: v_score
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment score for the V gene.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_score
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  v_identity:
    name: v_identity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Fractional identity for the V gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_identity
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  v_support:
    name: v_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_support
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  v_cigar:
    name: v_cigar
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CIGAR string for the V gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_cigar
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d_score:
    name: d_score
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment score for the first or only D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_score
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  d_identity:
    name: d_identity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Fractional identity for the first or only D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_identity
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  d_support:
    name: d_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_support
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  d_cigar:
    name: d_cigar
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CIGAR string for the first or only D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_cigar
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d2_score:
    name: d2_score
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment score for the second D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_score
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  d2_identity:
    name: d2_identity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Fractional identity for the second D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_identity
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  d2_support:
    name: d2_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_support
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  d2_cigar:
    name: d2_cigar
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CIGAR string for the second D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_cigar
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  j_score:
    name: j_score
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment score for the J gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_score
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  j_identity:
    name: j_identity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Fractional identity for the J gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_identity
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  j_support:
    name: j_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_support
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  j_cigar:
    name: j_cigar
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CIGAR string for the J gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_cigar
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  c_score:
    name: c_score
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment score for the C gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_score
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  c_identity:
    name: c_identity
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Fractional identity for the C gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_identity
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  c_support:
    name: c_support
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_support
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: float
  c_cigar:
    name: c_cigar
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CIGAR string for the C gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_cigar
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  v_sequence_start:
    name: v_sequence_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the V gene in the query sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_sequence_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  v_sequence_end:
    name: v_sequence_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the V gene in the query sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_sequence_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  v_germline_start:
    name: v_germline_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment start position in the V gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_germline_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  v_germline_end:
    name: v_germline_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment end position in the V gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_germline_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  v_alignment_start:
    name: v_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_alignment_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  v_alignment_end:
    name: v_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_alignment_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  d_sequence_start:
    name: d_sequence_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the first or only D gene in the query sequence.
      (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_sequence_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d_sequence_end:
    name: d_sequence_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the first or only D gene in the query sequence. (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_sequence_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d_germline_start:
    name: d_germline_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment start position in the D gene reference sequence for the
      first or only D gene (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_germline_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d_germline_end:
    name: d_germline_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment end position in the D gene reference sequence for the first
      or only D gene (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_germline_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d_alignment_start:
    name: d_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_alignment_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  d_alignment_end:
    name: d_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_alignment_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  d2_sequence_start:
    name: d2_sequence_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the second D gene in the query sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_sequence_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d2_sequence_end:
    name: d2_sequence_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the second D gene in the query sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_sequence_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d2_germline_start:
    name: d2_germline_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment start position in the second D gene reference sequence
      (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_germline_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d2_germline_end:
    name: d2_germline_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment end position in the second D gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_germline_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d2_alignment_start:
    name: d2_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the second D gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_alignment_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d2_alignment_end:
    name: d2_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the second D gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_alignment_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  j_sequence_start:
    name: j_sequence_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the J gene in the query sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_sequence_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  j_sequence_end:
    name: j_sequence_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the J gene in the query sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_sequence_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  j_germline_start:
    name: j_germline_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment start position in the J gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_germline_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  j_germline_end:
    name: j_germline_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment end position in the J gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_germline_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  j_alignment_start:
    name: j_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the J gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_alignment_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  j_alignment_end:
    name: j_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the J gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_alignment_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  c_sequence_start:
    name: c_sequence_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the C gene in the query sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_sequence_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  c_sequence_end:
    name: c_sequence_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the C gene in the query sequence (1-based closed
      interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_sequence_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  c_germline_start:
    name: c_germline_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment start position in the C gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_germline_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  c_germline_end:
    name: c_germline_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Alignment end position in the C gene reference sequence (1-based
      closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_germline_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  c_alignment_start:
    name: c_alignment_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Start position of the C gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_alignment_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  c_alignment_end:
    name: c_alignment_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: End position of the C gene alignment in both the sequence_alignment
      and germline_alignment fields (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_alignment_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  cdr1_start:
    name: cdr1_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1_start
    owner: Rearrangement
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr1_end:
    name: cdr1_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr1_end
    owner: Rearrangement
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr2_start:
    name: cdr2_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2_start
    owner: Rearrangement
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr2_end:
    name: cdr2_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr2_end
    owner: Rearrangement
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr3_start:
    name: cdr3_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3_start
    owner: Rearrangement
    domain_of:
    - Chain
    - SequenceDelineationV
    - Rearrangement
    range: integer
  cdr3_end:
    name: cdr3_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: CDR3 end position in the query sequence (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cdr3_end
    owner: Rearrangement
    domain_of:
    - Chain
    - Rearrangement
    range: integer
  fwr1_start:
    name: fwr1_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr1_start
    owner: Rearrangement
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr1_end:
    name: fwr1_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr1_end
    owner: Rearrangement
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr2_start:
    name: fwr2_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr2_start
    owner: Rearrangement
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr2_end:
    name: fwr2_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr2_end
    owner: Rearrangement
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr3_start:
    name: fwr3_start
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr3_start
    owner: Rearrangement
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr3_end:
    name: fwr3_end
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr3_end
    owner: Rearrangement
    domain_of:
    - SequenceDelineationV
    - Rearrangement
    range: integer
  fwr4_start:
    name: fwr4_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: FWR4 start position in the query sequence (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr4_start
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  fwr4_end:
    name: fwr4_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: FWR4 end position in the query sequence (1-based closed interval).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: fwr4_end
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  v_sequence_alignment:
    name: v_sequence_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Aligned portion of query sequence assigned to the V gene, including
      any indel corrections or numbering spacers.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_sequence_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  v_sequence_alignment_aa:
    name: v_sequence_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the v_sequence_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_sequence_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d_sequence_alignment:
    name: d_sequence_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Aligned portion of query sequence assigned to the first or only D
      gene, including any indel corrections or numbering spacers.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_sequence_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d_sequence_alignment_aa:
    name: d_sequence_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the d_sequence_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_sequence_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d2_sequence_alignment:
    name: d2_sequence_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Aligned portion of query sequence assigned to the second D gene,
      including any indel corrections or numbering spacers.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_sequence_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d2_sequence_alignment_aa:
    name: d2_sequence_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the d2_sequence_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_sequence_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  j_sequence_alignment:
    name: j_sequence_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Aligned portion of query sequence assigned to the J gene, including
      any indel corrections or numbering spacers.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_sequence_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  j_sequence_alignment_aa:
    name: j_sequence_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the j_sequence_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_sequence_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  c_sequence_alignment:
    name: c_sequence_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Aligned portion of query sequence assigned to the constant region,
      including any indel corrections or numbering spacers.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_sequence_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  c_sequence_alignment_aa:
    name: c_sequence_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the c_sequence_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_sequence_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  v_germline_alignment:
    name: v_germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_germline_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  v_germline_alignment_aa:
    name: v_germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the v_germline_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_germline_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d_germline_alignment:
    name: d_germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_germline_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d_germline_alignment_aa:
    name: d_germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the d_germline_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_germline_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d2_germline_alignment:
    name: d2_germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_germline_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  d2_germline_alignment_aa:
    name: d2_germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the d2_germline_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_germline_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  j_germline_alignment:
    name: j_germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_germline_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  j_germline_alignment_aa:
    name: j_germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the j_germline_alignment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_germline_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  c_germline_alignment:
    name: c_germline_alignment
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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).
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_germline_alignment
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  c_germline_alignment_aa:
    name: c_germline_alignment_aa
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Amino acid translation of the c_germline_aligment field.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: c_germline_alignment_aa
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: string
  junction_length:
    name: junction_length
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  junction_aa_length:
    name: junction_aa_length
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: junction_aa_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  np1_length:
    name: np1_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of nucleotides between the V gene and first D gene alignments
      or between the V gene and J gene alignments.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np1_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  np2_length:
    name: np2_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of nucleotides between either the first D gene and J gene
      alignments or the first D gene and second D gene alignments.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np2_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  np3_length:
    name: np3_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of nucleotides between the second D gene and J gene alignments.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: np3_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  n1_length:
    name: n1_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of untemplated nucleotides 5' of the first or only D gene
      alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: n1_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  n2_length:
    name: n2_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of untemplated nucleotides 3' of the first or only D gene
      alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: n2_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  n3_length:
    name: n3_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of untemplated nucleotides 3' of the second D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: n3_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  p3v_length:
    name: p3v_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of palindromic nucleotides 3' of the V gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: p3v_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  p5d_length:
    name: p5d_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of palindromic nucleotides 5' of the first or only D gene
      alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: p5d_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  p3d_length:
    name: p3d_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of palindromic nucleotides 3' of the first or only D gene
      alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: p3d_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  p5d2_length:
    name: p5d2_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of palindromic nucleotides 5' of the second D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: p5d2_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  p3d2_length:
    name: p3d2_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of palindromic nucleotides 3' of the second D gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: p3d2_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  p5j_length:
    name: p5j_length
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Number of palindromic nucleotides 5' of the J gene alignment.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: p5j_length
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  v_frameshift:
    name: v_frameshift
    annotations:
      nullable:
        tag: nullable
        value: true
    description: True if the V gene in the query nucleotide sequence contains a translational
      frameshift relative to the frame of the V gene reference sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: v_frameshift
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: boolean
  j_frameshift:
    name: j_frameshift
    annotations:
      nullable:
        tag: nullable
        value: true
    description: True if the J gene in the query nucleotide sequence contains a translational
      frameshift relative to the frame of the J gene reference sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: j_frameshift
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: boolean
  d_frame:
    name: d_frame
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d_frame
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  d2_frame:
    name: d2_frame
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: d2_frame
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  consensus_count:
    name: consensus_count
    annotations:
      nullable:
        tag: nullable
        value: true
    description: 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.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: consensus_count
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  duplicate_count:
    name: duplicate_count
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Copy number or number of duplicate observations for the query sequence.
      For example, the number of identical reads observed for this sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: duplicate_count
    owner: Rearrangement
    domain_of:
    - Rearrangement
    range: integer
  umi_count:
    name: umi_count
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: umi_count
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    range: integer
  cell_id:
    name: cell_id
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: cell_id
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Cell
    - CellExpression
    range: string
  clone_id:
    name: clone_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: clone_id
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - Clone
    - Tree
    range: string
  repertoire_id:
    name: repertoire_id
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: repertoire_id
    owner: Rearrangement
    domain_of:
    - AIRRSequencingAssay
    - Repertoire
    - RepertoireGroupDetail
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string
  sample_processing_id:
    name: sample_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sample_processing_id
    owner: Rearrangement
    domain_of:
    - Rearrangement
    - SampleProcessing
    range: string
  data_processing_id:
    name: data_processing_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: data_processing_id
    owner: Rearrangement
    domain_of:
    - DataProcessing
    - Alignment
    - Rearrangement
    - Clone
    - Cell
    - CellExpression
    range: string