C Cigar |
CIGAR string for the C gene alignment. |
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C Germline Alignment |
Aligned constant region germline sequence spanning the same region as the c_sequence_alignment field and including the same set of corrections and spacers (if any). |
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C Germline Alignment AA |
Amino acid translation of the c_germline_aligment field. |
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C IDentity |
Fractional identity for the C gene alignment. |
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C Region |
Constant region gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHG1*01 if using IMGT/GENE-DB). |
IGHG1*01 |
C Score |
Alignment score for the C gene alignment. |
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C Sequence Alignment |
Aligned portion of query sequence assigned to the constant region, including any indel corrections or numbering spacers. |
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C Sequence Alignment AA |
Amino acid translation of the c_sequence_alignment field. |
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C Support |
C gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the C gene assignment as defined by the alignment tool. |
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CDR1 |
Nucleotide sequence of the aligned CDR1 region. |
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CDR1 AA |
Amino acid translation of the cdr1 field. |
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CDR1 End |
CDR1 end position in the query sequence (1-based closed interval). |
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CDR1 Start |
CDR1 start position in the query sequence (1-based closed interval). |
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CDR2 |
Nucleotide sequence of the aligned CDR2 region. |
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CDR2 AA |
Amino acid translation of the cdr2 field. |
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CDR2 End |
CDR2 end position in the query sequence (1-based closed interval). |
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CDR2 Start |
CDR2 start position in the query sequence (1-based closed interval). |
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CDR3 |
Nucleotide sequence of the aligned CDR3 region. |
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CDR3 AA |
Amino acid translation of the cdr3 field. |
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CDR3 End |
CDR3 end position in the query sequence (1-based closed interval). |
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CDR3 Start |
CDR3 start position in the query sequence (1-based closed interval). |
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Cell Index |
Identifier defining the cell of origin for the query sequence. |
W06_046_091 |
Clone ID |
Clonal cluster assignment for the query sequence. |
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Complete Vdj |
True if the sequence alignment spans the entire V(D)J region. Meaning, sequence_alignment includes both the first V gene codon that encodes the mature polypeptide chain (i.e., after the leader sequence) and the last complete codon of the J gene (i.e., before the J-C splice site). This does not require an absence of deletions within the internal FWR and CDR regions of the alignment. |
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Consensus Count |
Number of reads contributing to the (UMI) consensus for this sequence. For example, the sum of the number of reads for all UMIs that contribute to the query sequence. |
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D Alignment End |
End position of the first or only D gene in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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D Alignment Start |
Start position of the first or only D gene in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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D Cigar |
CIGAR string for the first or only D gene alignment. |
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D Gene With Allele |
First or only D gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHD3-10*01 if using IMGT/GENE-DB). |
IGHD3-10*01 |
D Germline Alignment |
Aligned D gene germline sequence spanning the same region as the d_sequence_alignment field and including the same set of corrections and spacers (if any). |
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D Germline Alignment AA |
Amino acid translation of the d_germline_alignment field. |
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D Germline End |
Alignment end position in the D gene reference sequence for the first or only D gene (1-based closed interval). |
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D Germline Start |
Alignment start position in the D gene reference sequence for the first or only D gene (1-based closed interval). |
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D IDentity |
Fractional identity for the first or only D gene alignment. |
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D Score |
Alignment score for the first or only D gene alignment. |
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D Sequence Alignment |
Aligned portion of query sequence assigned to the first or only D gene, including any indel corrections or numbering spacers. |
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D Sequence Alignment AA |
Amino acid translation of the d_sequence_alignment field. |
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D Sequence End |
End position of the first or only D gene in the query sequence. (1-based closed interval). |
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D Sequence Start |
Start position of the first or only D gene in the query sequence. (1-based closed interval). |
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D Support |
D gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the first or only D gene as defined by the alignment tool. |
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D2 Alignment End |
End position of the second D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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D2 Alignment Start |
Start position of the second D gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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D2 Call |
Second D gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHD3-10*01 if using IMGT/GENE-DB). |
IGHD3-10*01 |
D2 Cigar |
CIGAR string for the second D gene alignment. |
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D2 Germline Alignment |
Aligned D gene germline sequence spanning the same region as the d2_sequence_alignment field and including the same set of corrections and spacers (if any). |
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D2 Germline Alignment AA |
Amino acid translation of the d2_germline_alignment field. |
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D2 Germline End |
Alignment end position in the second D gene reference sequence (1-based closed interval). |
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D2 Germline Start |
Alignment start position in the second D gene reference sequence (1-based closed interval). |
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D2 IDentity |
Fractional identity for the second D gene alignment. |
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D2 Score |
Alignment score for the second D gene alignment. |
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D2 Sequence Alignment |
Aligned portion of query sequence assigned to the second D gene, including any indel corrections or numbering spacers. |
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D2 Sequence Alignment AA |
Amino acid translation of the d2_sequence_alignment field. |
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D2 Sequence End |
End position of the second D gene in the query sequence (1-based closed interval). |
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D2 Sequence Start |
Start position of the second D gene in the query sequence (1-based closed interval). |
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D2 Support |
D gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the second D gene as defined by the alignment tool. |
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Data Processing ID |
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. |
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FWR1 |
Nucleotide sequence of the aligned FWR1 region. |
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FWR1 AA |
Amino acid translation of the fwr1 field. |
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FWR1 End |
FWR1 end position in the query sequence (1-based closed interval). |
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FWR1 Start |
FWR1 start position in the query sequence (1-based closed interval). |
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FWR2 |
Nucleotide sequence of the aligned FWR2 region. |
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FWR2 AA |
Amino acid translation of the fwr2 field. |
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FWR2 End |
FWR2 end position in the query sequence (1-based closed interval). |
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FWR2 Start |
FWR2 start position in the query sequence (1-based closed interval). |
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FWR3 |
Nucleotide sequence of the aligned FWR3 region. |
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FWR3 AA |
Amino acid translation of the fwr3 field. |
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FWR3 End |
FWR3 end position in the query sequence (1-based closed interval). |
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FWR3 Start |
FWR3 start position in the query sequence (1-based closed interval). |
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FWR4 |
Nucleotide sequence of the aligned FWR4 region. |
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FWR4 AA |
Amino acid translation of the fwr4 field. |
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FWR4 End |
FWR4 end position in the query sequence (1-based closed interval). |
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FWR4 Start |
FWR4 start position in the query sequence (1-based closed interval). |
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Gene Locus |
Gene locus (chain type). Note that this field uses a controlled vocabulary that is meant to provide a generic classification of the locus, not necessarily the correct designation according to a specific nomenclature. |
IGH |
Germline Alignment |
Assembled, aligned, full-length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any). |
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Germline Alignment AA |
Amino acid translation of the assembled germline sequence. |
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Germline Database |
Source of germline V(D)J genes with version number or date accessed. |
ENSEMBL, Homo sapiens build 90, 2017-10-01 |
J Alignment End |
End position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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J Alignment Start |
Start position of the J gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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J Cigar |
CIGAR string for the J gene alignment. |
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J Gene With Allele |
J gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHJ4*02 if using IMGT/GENE-DB). |
IGHJ4*02 |
J Germline Alignment |
Aligned J gene germline sequence spanning the same region as the j_sequence_alignment field and including the same set of corrections and spacers (if any). |
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J Germline Alignment AA |
Amino acid translation of the j_germline_alignment field. |
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J Germline End |
Alignment end position in the J gene reference sequence (1-based closed interval). |
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J Germline Start |
Alignment start position in the J gene reference sequence (1-based closed interval). |
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J IDentity |
Fractional identity for the J gene alignment. |
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J Score |
Alignment score for the J gene alignment. |
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J Sequence Alignment |
Aligned portion of query sequence assigned to the J gene, including any indel corrections or numbering spacers. |
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J Sequence Alignment AA |
Amino acid translation of the j_sequence_alignment field. |
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J Sequence End |
End position of the J gene in the query sequence (1-based closed interval). |
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J Sequence Start |
Start position of the J gene in the query sequence (1-based closed interval). |
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J Support |
J gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the J gene assignment as defined by the alignment tool. |
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Junction Length |
Number of nucleotides in the junction sequence. |
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Junction Length (AA) |
Number of amino acids in the junction sequence. |
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Junction/CDR3 AA |
Amino acid translation of the junction. |
CARAGVYDGYTMDYW |
Junction/CDR3 NT |
Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons. |
TGTGCAAGAGCGGGAGTTTACGACGGATATACTATGGACTACTGG |
N1 Length |
Number of untemplated nucleotides 5' of the first or only D gene alignment. |
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N2 Length |
Number of untemplated nucleotides 3' of the first or only D gene alignment. |
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N3 Length |
Number of untemplated nucleotides 3' of the second D gene alignment. |
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Np1 |
Nucleotide sequence of the combined N/P region between the V gene and first D gene alignment or between the V gene and J gene alignments. |
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Np1 AA |
Amino acid translation of the np1 field. |
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Np1 Length |
Number of nucleotides between the V gene and first D gene alignments or between the V gene and J gene alignments. |
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Np2 |
Nucleotide sequence of the combined N/P region between either the first D gene and J gene alignments or the first D gene and second D gene alignments. |
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Np2 AA |
Amino acid translation of the np2 field. |
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Np2 Length |
Number of nucleotides between either the first D gene and J gene alignments or the first D gene and second D gene alignments. |
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Np3 |
Nucleotide sequence of the combined N/P region between the second D gene and J gene alignments. |
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Np3 AA |
Amino acid translation of the np3 field. |
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Np3 Length |
Number of nucleotides between the second D gene and J gene alignments. |
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P3D Length |
Number of palindromic nucleotides 3' of the first or only D gene alignment. |
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P3D2 Length |
Number of palindromic nucleotides 3' of the second D gene alignment. |
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P3V Length |
Number of palindromic nucleotides 3' of the V gene alignment. |
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P5D Length |
Number of palindromic nucleotides 5' of the first or only D gene alignment. |
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P5D2 Length |
Number of palindromic nucleotides 5' of the second D gene alignment. |
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P5J Length |
Number of palindromic nucleotides 5' of the J gene alignment. |
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Productive |
True if the V(D)J sequence is predicted to be productive. |
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Read Count |
Copy number or number of duplicate observations for the query sequence. For example, the number of UMIs sharing an identical sequence or the number of identical observations of this sequence absent UMIs. |
123 |
Rearrangement ID |
Identifier for the Rearrangement object. May be identical to sequence_id, but will usually be a univerally unique record locator for database applications. |
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Rearrangement Set ID |
Identifier for grouping Rearrangement objects. |
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Repertoire ID |
Identifier to the associated repertoire in study metadata. |
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Rev Comp |
True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'. |
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Sample Processing ID |
Identifier to the sample processing object in the repertoire metadata for this rearrangement. If the repertoire has a single sample then this field may be empty or missing. If the repertoire has multiple samples then this field may be empty or missing if the sample cannot be differentiated or the relationship is not maintained by the data processing. |
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Sequence |
The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment. |
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Sequence AA |
Amino acid translation of the query nucleotide sequence. |
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Sequence Alignment |
Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement. |
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Sequence Alignment AA |
Amino acid translation of the aligned query sequence. |
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Sequence ID |
Unique query sequence identifier for the Rearrangment. 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. When downloaded from an AIRR Data Commons repository, this will usually be a universally unique record locator for linking with other objects in the AIRR Data Model. |
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Stop Codon |
True if the aligned sequence contains a stop codon. |
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V Alignment End |
End position of the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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V Alignment Start |
Start position of the V gene alignment in both the sequence_alignment and germline_alignment fields (1-based closed interval). |
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V Cigar |
CIGAR string for the V gene alignment. |
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V Gene With Allele |
V gene with allele. If referring to a known reference sequence in a database the relevant gene/allele nomenclature should be followed (e.g., IGHV4-59*01 if using IMGT/GENE-DB). |
IGHV4-59*01 |
V Germline Alignment |
Aligned V gene germline sequence spanning the same region as the v_sequence_alignment field and including the same set of corrections and spacers (if any). |
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V Germline Alignment AA |
Amino acid translation of the v_germline_alignment field. |
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V Germline End |
Alignment end position in the V gene reference sequence (1-based closed interval). |
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V Germline Start |
Alignment start position in the V gene reference sequence (1-based closed interval). |
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V IDentity |
Fractional identity for the V gene alignment. |
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V Score |
Alignment score for the V gene. |
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V Sequence Alignment |
Aligned portion of query sequence assigned to the V gene, including any indel corrections or numbering spacers. |
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V Sequence Alignment AA |
Amino acid translation of the v_sequence_alignment field. |
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V Sequence End |
End position of the V gene in the query sequence (1-based closed interval). |
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V Sequence Start |
Start position of the V gene in the query sequence (1-based closed interval). |
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V Support |
V gene alignment E-value, p-value, likelihood, probability or other similar measure of support for the V gene assignment as defined by the alignment tool. |
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Vj In Frame |
True if the V and J gene alignments are in-frame. |
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