IMGT/HighV-QUEST [1] (see also [2-5]) is the web portal of IMGT® [6], the international ImMunoGeneTics information system® (http://www.imgt.org) for the analysis of rearranged nucleotide sequences of the antigen receptors (immunoglobulins (IG) or antibodies and T cell receptors (TR)) [7, 8, 9] obtained from next generation sequencing (NGS), based on IMGT-ONTOLOGY [10] and the immunoinformatics IMGT scientific rules [11].

IMGT/HighV-QUEST [1, 3, 4] is the high-throughput version of IMGT/V-QUEST [12, 13] and can analyse thousands of immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences (up to 500 000 sequences) per run.

IMGT/HighV-QUEST uses the IMGT/V-QUEST program to analyse user sequences [5] and the IMGT/V-QUEST reference directory [6] (IMGT/V-QUEST documentation). IMGT/HighV-QUEST outputs have a content similar to that of IMGT/V-QUEST [5].

IMGT/HighV-QUEST statistical analysis is performed on IMGT/HighV-QUEST results selected by the user and include the characterization of the IMGT clonotype (AA) diversity and expression [4] and their comparison in up to one million sequences.

• All IMGT/HighV-QUEST users should be registered in order to be able to use this platform.
• IMGT/HighV-QUEST works with rearranged V-J and V-D-J sequences and germline V-GENE, but does not work with germline D-GENE or J-GENE.
• IMGT/HighV-QUEST can analyse sequences with DNA insertions or deletions (which do not respect the IMGT unique numbering). For more information, see 'Search for insertions and deletions'.
• IMGT/HighV-QUEST can analyse sequences containing two V domains (as scFv) if the option ‘Analysis of single chain Fragment variable (scFv)’ is selected in Advanced functionalities of the IMGT/HighV-QUEST Search page.
• IMGT/HighV-QUEST does not work with out-of-frame pseudogenes as they cannot be numbered according to the codon (or amino acid) IMGT unique numbering [14, 15]. You may use IMGT/BlastSearch (http://www.imgt.org/BlastSearch) in order to compare out-of-frame sequences against 'F+ORF+inframeP' genes and alleles IMGT reference sequences (select for 'Database' : 'IMGT/GENE-DB reference sequences').
• IMGT/HighV-QUEST does not work, or will give aberrant results, for too short partial sequences, sequences containing a cluster of V-GENE, or sequences with too long 5'UTR or 3'UTR.
  For these sequences, you may use IMGT/BlastSearch (http://www.imgt.org/BlastSearch) in order to identify the closest sequences from IMGT/LIGM-DB (select for 'Database' : 'IMGT/LIGM-DB') .

Once registered and registration accepted by the IMGT/HighV-QUEST administrator, users can log in to IMGT/HighV-QUEST using their e-mail address and the password they selected during the registration.
The first page that a user may see after logging in is the IMGT/HighV-QUEST Search Page.

IMGT/HighV-QUEST Search page comprises:

1. Selection and input
   
   

   Users must enter:

   - a title for their new analysis (50 characters or less).
   
   and select:
   
   - the species
   - the antigen receptor type (IG or TR) or the locus (for example, IGL)
   - the path to their local file to be submitted.
   
   Since IMGT/HighV-QUEST is designed for batches of large number of sequences, there is no copy/paste submission. The submitted file should contain IG or TR rearranged nucleotide sequences in FASTA format. The file must be formatted in text only (RTF or DOC formats are not accepted).
   
   Here are some examples of sequence files in FASTA format :
   Click here to get a FASTA file containing human IG sequences
   Click here to get a FASTA file containing human TR sequences
   
   Other sets of sequences to test the IMGT/HighV-QUEST functionalities are available here.
   
   Users can choose to receive an e-mail notification :
   • when the analysis is queued in the local analysis queue
   • when the analysis is submitted for computer processing
   • when the analysis is completed and the results can be downloaded
   • 5 days before the analysis is expired:
     15 days after their availability, the results will be definitively removed from the server. The expiration notification is not optional.
   
   
   
   
2. Display results
   
   
   The 'Display results' choice is identical to that of IMGT/V-QUEST (click here to see this part in IMGT/V-QUEST documentation).
   
   'Detailed view' will provide individual files (one file for each sequence analysed) as an option for submission < 150 000 sequences (click 'yes' for selecting the option). Individual files are not provided for submission > 150 000 sequences.
   
   'Files in CSV' will provide outputs with a content similar to that of the IMGT/V-QUEST Excel file sheets [9]. The 11 CSV files are selected by default. They should be kept selected if IMGT/HighV-QUEST statistical analysis is performed.




3. Advanced parameters
   
   
   The 'Advanced parameters' selection is identical to that of IMGT/V-QUEST (click here to see this part in IMGT/V-QUEST documentation).
   
   Note that: The option "Search for insertions and/or deletions" of Advanced parameters is selected by default.
   
   
   • Results with insertions
   • Results with deletions

1. Results file format
   
   IMGT/HighV-QUEST results consist of sequence analysis results in CSV text files. These files are archived together in a single file in .TXZ format. This format was chosen because of its common use. Users may use windows or other operating systems default archive tools (e.g., 7-zip) to extract (unzip) the files.
   
   
2. Results folders and files
   
   There are two folders:
   - the main folder with 11 (or 12, if scFv was selected) CSV files
   - the individual files folder
   
   
   
   
   
   
   
3. Results file contents



3.1 CSV files

If all options were selected in the IMGT/HighV-QUEST Search page (including ‘Analysis of single chain Fragment variable (scFv)’ in Advances Functionalities), the main folder contains 12 CSV files.


1. Summary (always provided in a spreadsheet and in a TXZ archive)
2. IMGT-gapped-nt-sequences
3. nt-sequences
4. IMGT-gapped-AA-sequences
5. AA-sequences
6. Junction
7. V-REGION-mutation-and-AA-change-table
8. V-REGION-nt-mutation-statistics
9. V-REGION-AA-change-statistics
10. V-REGION-mutation-hotspots
11. Parameters (always provided in a spreadsheet and in a txz archive)
12. scFv (only present if 'Analysis of single chain Fragment variable (scFv)' was selected in Advanced functionalities)

The Parameters.txt and Summary.txt files are always provided.

Note that:IMGT/HighV-QUEST statistical analysis can only be performed on results that include the 11 first CSV files.

The content of the CSV files is the same as that of the IMGT/V-QUEST Excel file sheets (click here to see this part in IMGT/V-QUEST documentation). For correspondence between the CSV file content and the IMGT/V-QUEST online display, see [5, 11]


3.2 Individual files

For submission < 150 000 sequences, the individual files are provided if the option has been selected by the user in 'Detailed View' of the IMGT/HighV-QUEST Search page.

One individual file is generated for each sequence analysed. Each individual file contains analysis results for the options selected by the user in 'Detailed View' of the IMGT/HighV-QUEST Search page.

On top of each individual file, the version of the IMGT/HighV-QUEST and IMGT/V-QUEST programs and of the IMGT/V-QUEST reference directory release are recalled.

The results of the individual files are the same as those of the IMGT/V-QUEST text results (click here to see this part in IMGT/V-QUEST documentation).


1. Alignments for V-GENE and allele identification
2. Alignments for D-GENE and allele identification
3. Alignments for J-GENE and allele identification
4. Results of IMGT/JunctionAnalysis
5. Sequence of the JUNCTION ('nt' and 'AA')
6. V-REGION alignment
7. V-REGION translation
8. V-REGION protein display
9. V-REGION mutation and AA change table
10. V-REGION mutation and AA change statistics
11. V-REGION mutation hotspots
12. Sequences of V-, V-J- or V-D-J- REGION ('nt' and 'AA') with gaps in FASTA
13. Annotation by IMGT/Automat

Note that: IMGT/StatClonotype works only with uploaded files (.txt format) from the IMGT/HighV-QUEST statistical analysis output ('stats_xxx' file available in 'data' directory of the IMGT/HighV-QUEST statistical analysis output where 'xxx' is the batch name and the locus type) as described IMGT/StatClonotype documentation. To get these files, you therefore need to launch the IMGT/HighV-QUEST statistical analysis.

1. 'Single IMGT V gene and allele name' used in IMGT/HighV-QUEST statistical analysis
   
   Some V genes and alleles are always found with identical results using IMGT/V-QUEST or IMGT/HighV-QUEST. This happens:
   • when the alleles only differ between them by nucleotide (nt) differences in 3' of the last codon of the V-REGION taken into account for the evaluation of the alignment score and closest GENE and allele identification (according to the IMGT unique numbering, codon 104 for IGH and the TR loci, codon 109 for IGK and IGI, and codon 110 for IGL),
   • when the alleles belong to duplicated genes with identical nucleotide sequences in the V-REGION analysed by IMGT/V-QUEST or IMGT/HighV-QUEST.
   
   In order to avoid the filtering-out of these sequences, the IMGT V gene and allele is assigned to a 'Single IMGT V gene and allele name' used in IMGT/HighV-QUEST statistical analysis (click here for the list).
   

2. Filtered-in and filtered-out sequences

   Total: sequences of the IMGT/HighV-QUEST output selected by the user and submitted to the statistical analysis.

   '1 copy': sequences in one copy, and therefore different by their length and/or their sequence, and retained in 'filtered-in' sequences.
   For each set of identical sequences, only one copy is retained in '1 copy' and the other redundant sequences for that copy are put into 'More than 1'.

   The following six categories are excluded from statistical analysis (filtered-out sequences):

   'More than 1': identical sequences (after that one copy of each one of identical sequences has been retained in '1 copy'). The 'More than 1' are excluded from the per se statistical analysis to avoid redundancy, the number of 'More than 1' being added to the corresponding '1 copy' ONLY at the end of statistical analysis.

   'No J-GENE': sequences for which IMGT/HighV-QUEST did not find any J-GENE, usually these sequences are very short in 3'.

   'No junction': sequences for which a junction could not be identified (e.g. no evidence of anchors).

   'Warnings': sequences with warnings for the V-REGION ('different CDR lengths' and/or 'id<85%').
   
   In the Warnings files:
   'different CDR lengths' means sequences with different AA lengths for CDR1-IMGT and/or CDR2-IMGT compared to the lengths of the CDR1-IMGT and/or CDR2-IMGT, respectively of the closest identified germline V gene and allele.
   'id<85%' means sequences with a V-REGION having a percent of identity <85% compared to the V-REGION of the closest identified germline V gene and allele.

   'Unknown functionality': sequences for which no functionality was detected.
   IMGT/HighV-QUEST is intended for the analysis of rearranged IG and TR sequences. The functionality identified by IMGT/HighV-QUEST is either 'productive' (no stop codon and in-frame junction) or 'unproductive' (stop codons, out-of-frame junction).

   

   The statistical analysis is performed on the '1 copy' category divided in two sets, depending on the IMGT/HighV-QUEST results:

   'single gene': only one gene identified by IMGT/HighV-QUEST.
   'Single gene' refers to V, D and J analysed separately or in combination.

   'several genes': several genes identified by IMGT/HighV-QUEST.
   'Several genes' refers to V, D and J analysed separately or in combination.
   
   

   'single allele': only one gene and allele identified by IMGT/HighV-QUEST.
   'Single allele' refers to V, D and J analysed separately or in combination.

   'several alleles (or genes)': several alleles (or genes) identified by IMGT/HighV-QUEST.
   'Several alleles (or genes)' refers to V, D and J analysed separately or in combination.
   
   

3. Definition of an 'IMGT clonotype (AA)'

   An 'IMGT clonotype (AA)' is defined by a unique V-(D)-J rearrangement (with IMGT gene and allele names determined by IMGT/HighV-QUEST at the nucleotide level) and a unique CDR3-IMGT AA (in-frame) junction sequence.
   
   Sequences assigned to an IMGT clonotype (AA) comprise:

   1. 'single allele' sequences with the same V and J genes and alleles and same CDR3-IMGT (AA).
   2. 'several alleles (or genes)' sequences with the same V and J genes and alleles among the different identified V and J genes and alleles and the same CDR3-IMGT (AA).
   3. sequences in 'More than 1' which have their '1 copy' among the sequences assigned to a given IMGT clonotype (AA).
   
   All sequences assigned to IMGT clonotypes (AA) are in-frame and have the conserved two anchors C104 and F/W118 (for example, F for TRB, W for IGH), V and J functional or ORF.
   
   IMGT clonotype (AA) representative sequence: each IMGT clonotype (AA) has a representative sequence chosen amongst the assigned sequences, the longest one and with the highest percentage of identity with the germline V gene and allele.
   
   
   
4. Definition of an 'IMGT clonotype (nt)'

   An IMGT clonotype (nt) is defined by a unique V-(D)-J rearrangement (with IMGT gene and allele names determined by IMGT/HighV-QUEST at the nucleotide level) and a unique CDR3-IMGT nt (in-frame) junction sequence.

   Several IMGT clonotypes nt may correspond to one IMGT clonotype (AA) if the CDR3-IMGT differ by one or more nucleotides from the CDR3-IMGT of the representative nucleotide sequence of the IMGT clonotype (AA).

1. Prerequisite

IMGT/HighV-QUEST statistical analysis can only be performed on results that include at least the first 11 (or 12, if scFv) CSV files (they should have been selected in 'Files in CSV' at the IMGT/HighV-QUEST Search page when launching the IMGT/HighV-QUEST analysis as shown in the screen capture below). For scFv, IMGT/HighV-QUEST statistics are provided per V-DOMAIN, independently.






2. Statistical analysis submission

Users must enter:

- a title for the statistical analysis
- define and select the batch or batches for the IMGT/HighV-QUEST statistical analysis. The total of sequences for a single batch is 500,000. The total of sequences for multiple batch is 1,000,000.
- Batch, is selected one by one from the user's 'Analysis history' page (the receptor type of all selected batches should be on the same locus)
- a batch ID for each analysis selected.





The statistical analysis can then be launched.

The IMGT/HighV-QUEST statistical output is provided as a txz file. After extraction of the archive, open the file "open_to_start.html" with a Web browser.
The IMGT/HighV-QUEST statistical output is organized in 6 sections :

1. 'Selected parameters' and 'Batch list table'
2. Result summary for batches
3. Result summary for IMGT clonotypes (AA)
4. Detailed results per batch
5. IMGT clonotype (AA) results comparison
6. 'data' directory






1. 'Selected parameters' and 'Batch list table'
   
   The 'Selected parameters' table recapitulates the parameters selected by the user at the statistical analysis submission. It provides the title, the species, the receptor type (or locus), IMGT reference directory set, Search for insertions/deletions ('yes' or 'no'), Nb of sequences (sum of all batches), Batch IMGT clonotype comparison ('yes' or 'no'), User notification (complete and/or expire) (complete: when the analysis is completed, expire: 15 days after the completion date), Analysis date (date and time), and Comments (submitted by the user).
   
   The 'Batch list table' displays for each batch, the batch ID (in orange) and as many lines as the number of IMGT/HighV-QUEST outputs selected by the user for a given batch. Each line displays the title of the selected IMGT/HighV-QUEST output, with the Nb of sequences, Species, Receptor type (or locus), IMGT/HighV-QUEST version, IMGT/V-QUEST version and IMGT/V-QUEST reference directory release.
   
   
   
   
   
   
2. Result summary for batches
   
   The 'Result summary for batches' table recapitulates, for each batch, the following:
   - Batch ID, Total (Nb of sequences in the selected batch) with average length (Avr Len).
   - then the different IMGT/HighV-QUEST sequence categories '1 copy', '1 copy' with indels, 'More than 1', 'More than 1' with indels, No J-GENE, No junction,Warnings, Unknown functionality, No results, with for each category, the number of sequences and the average length.
   
   
   
   
   
   
3. Result summary for IMGT clonotypes (AA)
   
   The 'Results summary for IMGT clonotypes (AA) table recapitulates for each batch (column 1), and then for each locus (column 2) the following:
   - Nb of IMGT clonotypes (AA) equal to the Nb of IMGT clonotypes (AA) representatives sequences),
   - Nb of sequences assigned to IMGT clonotypes (AA) (per definition in-frame), Nb of in-frame sequences not assigned to IMGT clonotypes (AA) (e.g. anchor AA changes), Nb of in-frame sequences,
   - Nb of in-frame productive sequences (no stop codons), Nb of in-frame unproductive sequences (stop codons),
   - Nb of out-of-frame sequences,
   - Nb of sequences '1 copy' + 'More than 1' (= Nb of analysed sequences),
   - Nb of 'single gene' and Nb of 'several genes'
   - then Nb of submitted sequences per batch.
   The percentage of nb of sequences '1 copy' + 'More than 1' is calculated versus the nb of submitted sequences. The percentage of all other columns is calculated versus nb of sequences '1 copy' + 'More than 1'.
   
   
   
   
   
   
4. Detailed results per batch
   
   
   They comprise two types of results:
   'Results categories' and V, D, J genes and alleles for genotype analysis ('1 copy' 'single gene' for V and J)
   IMGT clonotype (AA) and (nt) analysis results
   
   
   4.1 'Results categories' and V, D, J genes and alleles for genotype analysis ('1 copy' 'single gene' for V and J)
   
   4.1.1 Overview
   
   Results are archived in a single TXZ file called (stat_version_1.txz). A TXZ file is provided for each batch. When extracted, the TXZ file of each batch contains:
   • 5 reports in PDF
   • 1 README file
   • 1 'graphics' folder containing separate copy of graphical elements in PNG
   
   
   
   
   
   
   
   4.1.2 Content of the IMGT reports
   
   The content of the IMGT reports includes 9 sections:
   
   
   1. Comments
   2. Analysis list
   3. Summary table
   4. Terminology
   5. Number of '1 copy' with 'single gene' and 'several genes' (for V, D and/or J) tables and histograms
   6. '1 copy' with 'single gene' tables and histograms
   7. '1 copy' with 'several alleles (or genes)' gene and allele tables
   8. Sequences in 'More than 1'
   9. Other filtered-out sequences

   All sections are found in report 1 whereas reports 2 to 5 contains only part of them.

   1_IMGT_report_all.pdf: sections 1 to 9
   2_IMGT_report_summary.pdf: sections 1 to 5
   3_IMGT_report_1copy_single-gene.pdf: section 6
   4_IMGT_report_1copy_several-genes.pdf: section 7
   5_IMGT_report_filtered-out_sequences.pdf: sections 8 and 9
   
   
   
   
   
   1. Comments
      Comments are those added by the user in "Batch comments (optional)". In normal conditions the PDF documents are not editable, therefore, this functionality was added in IMGT/HighV-QUEST to give users the possibility to include some optional comments in the final report in order to be able to recognize it later.
      
      
   2. Analysis list
      'Analyses list' recapitulates the list of IMGT/HighV-QUEST sets analysed with title, Nb of sequences, IMGT/HighV-QUEST reference directory (species and receptor type or locus), IMGT/HighV-QUEST version, IMGT/V-QUEST version and IMGT/V-QUEST reference directory release.
      
      Note that: IMGT/HighV-QUEST and the IMGT/V-QUEST versions and the IMGT/V-QUEST reference directory release are important information for statistical analysis. To check the details of each version and upgrade:
      IMGT/HighV-QUEST Upgrades and versions, IMGT/V-QUEST reference directory releases, IMGT/V-QUEST program versions pages.
      
      
      
      
      
      
      
   3. Summary table
      The Summary table shows the chosen parameters for the statistical analysis and the categories of sequences as identified and filtered by IMGT/HighV-QUEST with Nb of sequences abd sequence average length (nt) for each category. The IMGT/HighV-QUEST statistical analysis is performed only on the filtered-in sequences ('1 copy').
      
      
      
      Statistical analysis is done on '1 copy'. The 'More than 1' sequences are aggreagted to the '1 copy' at the end of the statistical analysis once it has been performed on the '1 copy'. Filtered-out sequences include 'No J-GENE', 'No JUNCTION', 'Warnings', 'Unknown functionalities' and 'No results'.
      
      
      
      
   4. Terminology
      Same as above. This section helps users understand the general terminology of the statistical analysis report.
      
      
   5. Number of '1 copy' with 'single gene' and 'several genes' (for V, D and/or J) tables and histograms
      These tables and histograms show, for each locus, the number sequences for which IMGT/HighV-QUEST has found 'single gene' and 'several genes', respectively, either for each gene type, separately (V, D, J) or in combination ('V,D', 'D,J', 'V,J', 'V,D,J').
      
      
      
      
      
      
      
   6. '1 copy' with 'single gene' gene and allele tables and histograms
      The tables show the IMGT gene and allele name, the number of '1 copy' (Total), Sequence average length (in nb of nt), V-REGION average length (in nb of nt), 'id=100%' which represents the number of sequences with an identity percent of 100% by comparison with the germline.
      The colored lines (green: V, red: D, yellow: J) display the results per gene. For each gene, the results are then displayed per allele (white lines), with the indication of the functionality of the germline allele and for id=100%, and between parentheses, percent of these sequences by comparison to 'Total'.
      The functionality of an allele can be:
      • F: Functional
      • P: Pseudogene
      • ORF: Open Reading Frame
      The functionality is shown between parentheses, (F) and (P), when the corresponding germline gene has not yet been isolated.
      It is shown between brackets, [F] and [P], when it is not known if the sequence is germline or rearranged.
      
      
      
      
      
      
      
      Histograms display the number of '1 copy' with 'single gene' for each V, (D) and J genes. Genes are shown according to their position from 5' to 3' in the concerned locus. Unmapped genes are located at the top of the histograms.
      
      
      
      
      
      
      
   7. '1 copy' with 'several genes' gene and allele tables
      These tables have the same header and the same type of results as '6'.
      There are as many different lines as different results, as proposed by IMGT/HighV-QUEST, at the gene (colored lines) and/or allele level (white lines).
      These results are usually obtained for short sequences which do not allow the assignment by IMGT/HighV-QUEST to a single gene or single allele.
      
      
      
      
      
      
      
   8. Sequences in 'More than 1'
      Sequences in 'More than 1' (violet-blue lines) are shown below each corresponding '1 copy' (green lines). The 'More than 1' are excluded from the per se statistical analysis to avoid redundancy, the number of 'More than 1' being added to the corresponding '1 copy' ONLY at the end of statistical analysis.
      
      
      
      
      
      
      
   9. Other filtered-out sequences
      All other filtered-out sequences ('No J-GENE', 'No junction', 'Warnings', 'Unknown functionality', and 'No results') are provided in separate similar tables, with the 'Sequence number' and the 'Sequence ID'.
      
      
      
      
      
      
      
   4.2 IMGT clonotype (AA and nt) results per locus
   
   Overview IMGT clonotype (AA and nt) results per locus are provided in 10 sections (HTML pages):
   
   
   1. IMGT clonotypes (AA) per Nb
   2. IMGT clonotypes (AA) per Nb with detailed clonotypes (nt)
   3. IMGT clonotypes (AA) per V gene
   4. IMGT clonotypes (AA) per V gene with detailed clonotypes (nt)
   5. IMGT clonotypes (AA) per CDR3-IMGT length (AA)
   6. IMGT clonotypes (AA) per CDR3-IMGT length (AA) with detailed clonotypes (nt)
   7. IMGT clonotypes (AA) by CRD3-IMGT sequence (AA) alphabetical order with detailed clonotypes (nt)
   8. IMGT clonotype (AA) diversity and expression histograms: per V, (D), J-GENE and per CDR3-IMGT length
   9. IMGT clonotype (AA) diversity and expression tables: per V, (D), J-GENE and per CDR3-IMGT length
   10. V gene and allele table: Rearrangements, Nb of sequences and Nb IMGT clonotypes (AA) per V-GENE and allele
   
   
   
   4.2.1 IMGT clonotypes (AA) per Nb
   

   The Nb of IMGT clonotypes (AA) is given by the total number of ID (last line in column #).
   The 'IMGT clonotypes (AA) per Nb' provides for each IMGT clonotype (AA):

   • ID, nb (#) and experimental ID (Exp. ID).
   • Nb, Nb of '1 copy', Nb of 'More than 1' and Total (=nb of sequences assigned to that IMGT clonotype (AA)).
   • IMGT clonotype (AA) definition: V, D and J genes and alleles, CDR3-IMGT length (AA), CDR3-IMGT sequences (AA), Anchors 104, 118.
   • IMGT clonotype (AA) representative sequence: V % (percentage of identity of the V-REGION compared to the closest germline V gene), Sequence length, Functionnality (as identified by IMGT/HighV-QUEST), Sequence ID with link to the file of the representative sequence.
   • IMGT clonotypes (nt): Sequences file ('1 copy') with a link to each 'Sequences file' containing the '1 copy' sequences in FASTA format assigned to a given IMGT clonotype (AA).
   
   In this table, the results are sorted by decreasing nb of '1 copy' and then by decreasing nb of 'More than 1'.
   
   
   
   
   
   
   4.2.2 IMGT clonotypes (AA) per Nb with detailed clonotypes (nt)
   

   The Nb of IMGT clonotypes (AA) is given by the total number of ID (last line in column #).
   The same information, as in IMGT clonotypes (AA) per Nb, is provided for each IMGT clonotype (AA) and displayed in the pink line, with under each clonotype (AA), the corresponding IMGT clonotype(s) (nt) displayed on separate lines.
   
   The following information is provided:

   • ID nb (the same as that of the IMGT clonotype (AA)) (#),
   • CDR3-IMGT length (nt),
   • nb of different CDR3-IMGT (nt),
   
   and then, for each CDR3-IMGT (nt):
   
   
   • CDR3-IMGT sequence (nt),
   • nb of different nt in the CDR3 (compared to the sequence (nt) of the IMGT clonotype (AA)),
   • V gene and allele, D gene and allele, J gene and allele,
   • Anchors 104,118: 'C,F' or 'C,W',
   • V-REGION identity % mean, V-REGION length mean,
   • J-REGION identity % mean, J-REGION length mean,
   • Sequence length mean,
   • nb of '1 copy', nb of 'More than 1' and Total (=nb of sequences assigned to that IMGT clonotype (nt) (the 3 columns on the right)). For a given IMGT clonotype AA the sum of '1 copy', 'More than 1', and Total of the IMGT clonotypes (nt) is equal respectively to those of the IMGT clonotype (AA) (boxes 3, 4, 5 of the pink line).
   
   
   
   
   
   
   4.2.3 IMGT clonotypes (AA) per V gene
   

   The same information, as IMGT clonotypes (AA) per Nb, is provided but sorted here alphabetically by V gene and allele name.

   
   
   
   
   
   
   4.2.4 IMGT clonotypes (AA) per V gene with detailed clonotypes (nt)
   

   The same information, as IMGT clonotypes (AA) per Nb with detailed clonotypes (nt), is provided but sorted here alphabetically by V gene and allele name.
   For a given IMGT clonotype AA, the sum of '1 copy', 'More than 1', and Total of the IMGT clonotypes (nt) is equal respectively to the pink boxes before sequence file.

   
   
   
   
   
   
   4.2.5 IMGT clonotypes (AA) per CDR3-IMGT length (AA)
   

   The same information, as IMGT clonotypes (AA) per Nb, is provided but sorted here by CDR3-IMGT length.
   This display allows identification of sequences assigned to different IMGT clonotypes (AA) whereas, most probably, they represent a single IMGT clonotype (AA).

   
   
   
   
   
   
   4.2.6 IMGT clonotypes (AA) per CDR3-IMGT length (AA) with detailed clonotypes (nt)
   

   The same information, as IMGT Clonotypes (AA) per Nb, is provided with detailed clonotypes (nt) sorted by CDR3-IMGT length (AA) and, under a same length, by CDR3-IMGT sequence (AA) alphabetical order.

   
   
   
   
   
   
   4.2.7 IMGT clonotypes (AA) by CRD3-IMGT sequence (AA) alphabetical order with detailed clonotypes (nt)
   

   The same information, as IMGT clonotypes (AA) per Nb with detailed clonotypes (nt), is provided sorted by CRD3-IMGT sequence (AA) alphabetical order following a decreasing CDR3-IMGT length. The format of the table is the same as in 6. IMGT Clonotypes (AA) per CDR3-IMGT length (AA) with detailed clonotypes (nt).

   
   
   
   
   
   
   4.2.8 IMGT clonotype (AA) diversity and expression histograms: per V, (D), J-GENE and per CDR3-IMGT length
   

   - IMGT clonotype (AA) diversity histograms: Nb of IMGT clonotype (AA) per V-GENE (green color), D-GENE (for IGH, TRB, TRD) (red color) and J-GENE (yellow color) and per CDR3-IMGT length.
   - IMGT clonotype (AA) expression histograms: Nb of sequences assigned to an IMGT clonotype (AA) per V-GENE, D-GENE (for IGH, TRB, TRD) and J-GENE (pink color).
   - IMGT clonotype (AA) histograms per CDR3-IMGT length.

   
   
   4.2.9 IMGT clonotype (AA) diversity and expression tables: per V, (D), J-GENE and per CDR3-IMGT length
   

   - IMGT clonotype (AA) diversity table: Nb of IMGT clonotypes (AA) per V-GENE, D-GENE (for IGH, TRB, TRD), J-GENE.
   - IMGT clonotype (AA) expression table: Nb of sequences assigned to an IMGT clonotype (AA) per V-GENE, D-GENE (for IGH, TRB, TRD), J-GENE.
   - IMGT clonotypes (AA) table per CDR3-IMGT length.

   
   
   4.2.10 V gene and allele table rearrangements
   

   The table shows for each V gene name and V allele name:

   • Nb of sequences assigned to an IMGT clonotype (AA),
   • Nb of different IMGT clonotypes (AA),
   • Nb of out-of-frame sequences,
   • Nb of other categories sequences.
   
   Clicking on the red and yellow squares, in the "V gene name" and "V allele name" columns, gives access to the D and J genes and alleles, respectively, involved in the rearrangements of a given V gene or allele.
   
   
   
   
   
   
   
5. IMGT clonotype (AA) results comparison
   
   They include the following results per locus:
   • IMGT clonotypes (AA) comparison: Full results
   • IMGT clonotypes (AA) comparison: Synthesis table
   • IMGT clonotypes (AA) comparison: Result summary table per V-GENE, D-GENE (for IGH, TRB, TRD), J-GENE
   
   
   5.1 IMGT clonotypes (AA) comparison: Full results

   The same presntation, as 'IMGT clonotypes (AA) per CDR3-IMGT length (AA)' is provided but sorted here by IMGT clonotypes (AA) present in a single batch ("Present in MID1", lightblue and lightsteel blue lines) and IMGT clonotypes (AA) common to 2 (or more) batches ("Present in MID1 and MID2", lightpink and light yellow lines).
   The information is paginated by page size and by different batch combination and their common IMGT clonotypes (AA).

   
   
   
   
   
   
   5.2 IMGT clonotypes (AA) comparison: Synthesis table

   The Synthesis table indicates the number of IMGT clonotypes (AA) (diversity) and the number of sequences assigned to IMGT clonotypes (AA) (expression) only present ('exclusive') in a single batch or common to two or more batches.
   There is one line for each single batch (Nb of batches: 1) and for each combination of batches (Nb of batches: 2 or >2).

   
   
   
   
   
   
   5.3 IMGT clonotypes (AA) comparison: Result summary table per V-GENE, D-GENE (for IGH, TRB, TRD), J-GENE

   The table recapitulates per gene of each batch:

   • 'Nb of IMGT clonotypes (AA)'
   • 'Nb of in-frame sequences assigned to IMGT clonotypes (AA)'.
   
   The order of genes is the same as in the locus, with unmapped genes in the first lines.
   
   
   
   
   
   
   
6. 'data' directory
   
   The 'data' directory contains the 'stats_xxx' (.txt format) file(s) where 'xxx' is the batch name and the locus type.
   
   At least two 'stats_xxx' files are needed to launch a comparative analysis in IMGT/StatClonotype tool.
   
   This file contains 26 columns (see Table Content of the stats_xxx file below).
   
   
   
   
   
   
   

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