VDJ Dominant Contigs AIRR
File: [sample_name]_VDJ_Dominant_Contigs_AIRR.tsv
Putative cells only, dominant contig for each CellID–chain combination. DBEC adjustment is applied. The file is compliant with the AIRR rearrangement schema and contains additional informational columns in addition to all the mandatory ones.
Data columns: Cell Identifiers, Read and Molecule counts, Full trimmed contig nucleotide and amino acid sequence, Framework and CDR region nucleotide and amino acid sequence, V, D, J, and C gene segments, full length and productive status.
Refer to docs.airr-community.org/en/stable/datarep/rearrangements.html
This file is only output when the experiment included an appropriate TCR/BCR assay, and the VDJ_Version option is
selected.
| Metric | Definition | Major contributing factors |
|---|---|---|
| cell_id | Unique cell ID for the cell represented by this row. Cell index will match between VDJ data and gene/AbSeq expression data tables | Sequencing qualityLibrary quality |
| cell_type_experimental | Inferred cell type. Cell type is inferred, either from mRNA targeted panel expression data or from relative counts of BCR vs TCR | Sample type mRNA Panel |
| high_quality_cell | True/False - This cell was designated as high quality, having a B or T type, a productive contig, and sufficient VDJ molecules | Sample qualityLibrary quality |
| locus | Type of VDJ sequence: one of TRA, TRB, TRG, TRD, IGH, IGK, and IGL | Cell viabilityLibrary quality |
| sequence_id | Unique ID for contig formatted as [cell_id]_[locus]_[number] | Sequencing qualityLibrary quality |
| consensus_count | Number of reads for this contig | Cell viabilityLibrary quality |
| umi_count | Number of unique molecules (UMI) for this contig. Previously called "duplicate_count" in an earlier AIRR standard | Cell viabilityLibrary quality |
| sequence | Assembled nucleotide sequence of contig after trimming | Library qualityVDJ recombination |
| sequence_length | Length of full contig nucleotide sequence after trimming | Library qualityVDJ recombination |
| sequence_aa | Amino acid sequence of contig after trimming | Library qualityVDJ recombination |
| sequence_aa_length | Length of full contig amino acid sequence after trimming | Library qualityVDJ recombination |
| sequence_alignment | Nucleotide sequence corresponding to VDJ coding region after trimming | VDJ recombination |
| sequence_alignment_length | Length of nucleotide sequence corresponding to VDJ coding region after trimming | VDJ recombination |
| sequence_alignment_aa | Amino acid sequence corresponding to VDJ coding region after trimming | VDJ recombination |
| sequence_alignment_aa_length | Length of amino acid sequence corresponding to VDJ coding region after trimming | VDJ recombination |
| junction | Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons | VDJ recombination |
| junction_aa | Amino acid translation of the junction | VDJ recombination |
| productive | True/False — there are no stop codons in the protein-coding portion of the sequence | VDJ recombination |
| rev_comp | True/False — the alignment is on the opposite strand (reverse complemented) with respect to the contig sequence. This field is always False for contig sequences from the BD Rhapsody VDJ library | Sequencing qualityLibrary quality |
| complete_VDJ | True/False — this cell chain combination contains some amino acid sequence for each framework (FR1-FR4) region and each CDR (1-3) region | Library qualityVDJ recombination |
| v_call | V gene segment identified for this contig | VDJ recombination |
| v_support | Quality of V gene alignment - lower is better | Sequencing qualityLibrary quality |
| v_cigar | CIGAR string for the V gene alignment | VDJ recombination |
| v_sequence_start | Start position of the V gene in the contig sequence (1-based closed interval) | VDJ recombination |
| v_sequence_end | End position of the V gene in the contig sequence (1-based closed interval) | VDJ recombination |
| d_call | First or only D gene segment identified for this contig | VDJ recombination |
| d_support | Quality of D gene alignment, lower is better | Sequencing qualityLibrary quality |
| d_cigar | CIGAR string for the D gene alignment | VDJ recombination |
| d_sequence_start | Start position of the D gene in the contig sequence (1-based closed interval) | VDJ recombination |
| d_sequence_end | End position of the D gene in the contig sequence (1-based closed interval) | VDJ recombination |
| j_call | J gene segment identified for this contig | VDJ recombination |
| j_support | Quality of J gene alignment - lower is better | Sequencing qualityLibrary quality |
| j_cigar | CIGAR string for the J gene alignment | VDJ recombination |
| j_sequence_start | Start position of the J gene in the contig sequence (1-based closed interval) | VDJ recombination |
| j_sequence_end | End position of the J gene in the contig sequence (1-based closed interval) | VDJ recombination |
| c_call | C gene segment identified for this contig | VDJ recombination |
| fwr1 | Nucleotide sequence of the FR1 for the contig | VDJ recombination |
| fwr1_aa | Amino acid sequence of the FR1 for the contig | VDJ recombination |
| fwr2 | Nucleotide sequence of the FR2 for the contig | VDJ recombination |
| fwr2_aa | Amino acid sequence of the FR2 for the contig | VDJ recombination |
| fwr3 | Nucleotide sequence of the FR3 for the contig | VDJ recombination |
| fwr3_aa | Amino acid sequence of the FR3 for the contig | VDJ recombination |
| fwr4 | Nucleotide sequence of the FR4 for the contig | VDJ recombination |
| fwr4_aa | Amino acid sequence of the FR4 for the contig | VDJ recombination |
| cdr1 | Nucleotide sequence of the CDR1 for the contig | VDJ recombination |
| cdr1_aa | Amino acid sequence of the CDR1 for the contig | VDJ recombination |
| cdr2 | Nucleotide sequence of the CDR2 for the contig | VDJ recombination |
| cdr2_aa | Amino acid sequence of the CDR2 for the contig | VDJ recombination |
| cdr3 | Nucleotide sequence of the CDR3 for the contig | VDJ recombination |
| cdr3_aa | Amino acid sequence of the CDR3 for the contig | VDJ recombination |
| germline_alignment | Assembled, aligned, full-length inferred germline sequence spanning the same region as the sequence_alignment field | VDJ recombination |
| germline_alignment_aa | Amino acid translation of the assembled germline sequence | VDJ recombination |
| 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) | VDJ recombination |
| v_germline_alignment_aa | Amino acid translation of the v_germline_alignment field | VDJ recombination |
| 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) | VDJ recombination |
| d_germline_alignment_aa | Amino acid translation of the d_germline_alignment field | VDJ recombination |
| 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) | VDJ recombination |
| j_germline_alignment_aa | Amino acid translation of the j_germline_alignment field | VDJ recombination |
| v_germline_start | Alignment start position in the V gene reference sequence (1-based closed interval) | VDJ recombination |
| v_germline_end | Alignment end position in the V gene reference sequence (1-based closed interval) | VDJ recombination |
| d_germline_start | Alignment start position in the D gene reference sequence for the first or only D gene (1-based closed interval) | VDJ recombination |
| d_germline_end | Alignment end position in the D gene reference sequence for the first or only D gene (1-based closed interval) | VDJ recombination |
| j_germline_start | Alignment start position in the J gene reference sequence (1-based closed interval) | VDJ recombination |
| j_germline_end | Alignment end position in the J gene reference sequence (1-based closed interval) | VDJ recombination |
| np1_length | Nucleotide sequence length of the combined N/P region between the V gene and first D gene alignment or between the V gene and J gene alignments | VDJ recombination |
| np2_length | Nucleotide sequence length 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 | VDJ recombination |
VDJ Unfiltered Contigs AIRR
File: [sample_name]_VDJ_Unfiltered_Contigs_AIRR.tsv
All cell IDs, all assembled contigs that were successfully annotated.
The file is compliant with the AIRR rearrangement schema and contains additional informational columns in addition to all the mandatory ones.
Data columns: Cell Identifiers, Read and Molecule counts, Full trimmed contig nucleotide and amino acid sequence, Framework and CDR region nucleotide and amino acid sequence, V, D, J, and C gene segments, full length, and productive status.
Refer to docs.airr-community.org/en/stable/datarep/rearrangements.html
Shared column definitions are identical to the VDJ_Dominant_Contigs_AIRR.tsv file. Here are listed the columns unique to this file.
| Metric | Definition | Major contributing factors |
|---|---|---|
| Dominant | True/False — this contig was selected as the dominant contig for this cell-chain combination. | Library qualityVDJ recombination |
| Putative_ Cell | True/False — this cell index was selected as a putative cell based on the mRNA panel. | Cell viabilitymRNA panel |