Alignment Schema (Experimental)

See the format overview for details on how to structure this data.

Note, this schema definition is still experimental and should not be considered final.

Fields

Download as TSV.

Name Type Priority Description
sequence_id string required Unique query sequence identifier within the file. 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.
segment string required The segment for this alignment. One of V, D, J or C.
rev_comp boolean optional Alignment result is from the reverse complement of the query sequence.
call string required Gene assignment with allele.
score number required Alignment score.
identity number optional Alignment fractional identity.
support number optional Alignment E-value, p-value, likelihood, probability or other similar measure of support for the gene assignment as defined by the alignment tool.
cigar string required Alignment CIGAR string.
sequence_start integer optional Start position of the segment in the query sequence (1-based closed interval).
sequence_end integer optional End position of the segment in the query sequence (1-based closed interval).
germline_start integer optional Alignment start position in the reference sequence (1-based closed interval).
germline_end integer optional Alignment end position in the reference sequence (1-based closed interval).
rank integer optional Alignment rank.
rearrangement_id string optional Identifier for the Rearrangement object. May be identical to sequence_id, but will usually be a univerally unique record locator for database applications.
data_processing_id string optional 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.
germline_database string optional Source of germline V(D)J genes with version number or date accessed.