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¶
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. |
rearrangement_set_id |
string |
optional | Identifier for grouping Rearrangement objects. |
germline_database |
string |
optional | Source of germline V(D)J genes with version number or date accessed. For example, ‘IMGT/GENE-DB 3.1.18 (15 March 2018)’. |