[[alignment-output-files-summary]]
Alignment output files summary
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Upon alignment the alignment parameters/dates/filenames will appended to
the _aligns/aligns_info.out_ file for easy traceability.

Alignment files are semicolon separated files. For each alignment of a
genomic template to a sequence the following fields are given:

[width="99%",cols="<32%,<68%",options="header",]
|=======================================================================
|Field |Description
|seq_index |The sequence index the alignment corresponds to in the
_indexed_sequences.csv_ file.

|gene_name |The gene name as provided in the genomic template file

|score |SW alignment score

|offset |The index of the first letter of the (undeleted) genomic
template on the read as described in the previous section. Indices are 0 based.

|insertions |Indices of the alignment inserted nucleotides (relative to
the read)

|deletions |Indices of the alignment deleted nucleotides (relative to
the genomic template)

|mismatches |Indices of the alignment mismatches (relative to the read)

|length |Length of the SW alignment (including insertions and deletions)

|5_p_align_offset |Offset of the first nucleotide of the SW alignment
(relative to the read)

|3_p_align_offset |Offset of the last nucleotide of the SW alignemnt
(relative to the read)
|=======================================================================



The CDR3 files are semicolon separated files. For each IGoR indexed 
sequence the following fields are given:
[width="99%",cols="<32%,<68%",options="header",]
|=======================================================================
|Field |Description
|seq_index |The sequence index the alignment corresponds to in the
_indexed_sequences.csv_ file.

|v_anchor | Position of the V anchor (first nucleotide of 2nd-CYS codon) relative to the read sequence. 

|j_anchor | Position of the J anchor (last nucleotide of J-PHE or J-TRP codon) relative to the read sequence. 

|CDR3nt | Nucleotide CDR3 sequence of the indexed sequence.

|CDR3aa | Amino acids CDR3 sequence of the indexed sequence.

|=======================================================================

TIP: Anchors positions are 0 based indices relative to the read sequence.
