Clone and Lineage Tree Schema (Experimental)

A unique inferred clone object that has been constructed within a single data processing for a single repertoire and a subset of its sequences and/or rearrangements.

A clone object may have one or more inferred lineage trees. Each tree is represented by a Newick string for its edges and a dictionary of node objects.

File Format Specification

The file format has not been specified yet.

Clone Fields

Download as TSV

Name	Type	Attributes	Definition
clone_id	string	required, identifier, nullable	Identifier for the clone.
repertoire_id	string	optional, nullable	Identifier to the associated repertoire in study metadata.
data_processing_id	string	optional, nullable	Identifier of the data processing object in the repertoire metadata for this clone.
sequences	array of string	optional, nullable	List sequence_id strings that act as keys to the Rearrangement records for members of the clone.
v_call	string	optional, nullable	V gene with allele of the inferred ancestral of the clone. For example, IGHV4-59*01.
d_call	string	optional, nullable	D gene with allele of the inferred ancestor of the clone. For example, IGHD3-10*01.
j_call	string	optional, nullable	J gene with allele of the inferred ancestor of the clone. For example, IGHJ4*02.
junction	string	optional, nullable	Nucleotide sequence for the junction region of the inferred ancestor of the clone, where the junction is defined as the CDR3 plus the two flanking conserved codons.
junction_aa	string	optional, nullable	Amino acid translation of the junction.
junction_length	integer	optional, nullable	Number of nucleotides in the junction.
junction_aa_length	integer	optional, nullable	Number of amino acids in junction_aa.
germline_alignment	string	required, nullable	Assembled, aligned, full-length inferred ancestor of the clone spanning the same region as the sequence_alignment field of nodes (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 germline_alignment.
v_alignment_start	integer	optional, nullable	Start position in 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 in the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
d_alignment_start	integer	optional, nullable	Start position of the D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval).
d_alignment_end	integer	optional, nullable	End position of the D gene alignment in both the sequence_alignment and germline_alignment fields (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).
junction_start	integer	optional, nullable	Junction region start position in the alignment (1-based closed interval).
junction_end	integer	optional, nullable	Junction region end position in the alignment (1-based closed interval).
umi_count	integer	optional, nullable	Number of distinct UMIs observed across all sequences (Rearrangement records) in this clone.
clone_count	integer	optional, nullable	Absolute count of the size (number of members) of this clone in the repertoire. This could simply be the number of sequences (Rearrangement records) observed in this clone, the number of distinct cell barcodes (unique cell_id values), or a more sophisticated calculation appropriate to the experimental protocol. Absolute count is provided versus a frequency so that downstream analysis tools can perform their own normalization.
seed_id	string	optional, nullable	sequence_id of the seed sequence. Empty string (or null) if there is no seed sequence.

Tree Fields

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Name	Type	Attributes	Definition
tree_id	string	required, identifier, nullable	Identifier for the tree.
clone_id	string	required, nullable	Identifier for the clone.
newick	string	required, nullable	Newick string of the tree edges.
nodes	object	optional, nullable	Dictionary of nodes in the tree, keyed by sequence_id string

Node Fields

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Name	Type	Attributes	Definition
sequence_id	string	required, identifier, nullable	Identifier for this node that matches the identifier in the newick string and, where possible, the sequence_id in the source repertoire.
sequence_alignment	string	optional, nullable	Nucleotide sequence of the node, aligned to the germline_alignment for this clone, including including any indel corrections or spacers.
junction	string	optional, nullable	Junction region nucleotide sequence for the node, where the junction is defined as the CDR3 plus the two flanking conserved codons.
junction_aa	string	optional, nullable	Amino acid translation of the junction.