Table 3:
Sequence-level fields included in the immunoSEQ Analyzer for immunoSEQ data.
| Total Templates (Sum) | total_templates | integer | The sum of template counts for all productive and unproductive rearrangements in the sample. Expect this value to be slightly larger than Total Templates (Aggregate) found in immunoSEQ Analyzer due to rounding of template counts for individual rearrangements. |
| Total Productive Templates (Sum) | productive_templates | integer | The sum of template counts for all productive rearrangements in the sample. Expect this value to be different than Total T cells, due to rounding of template counts for individual rearrangements. |
| Rearrangements | total_rearrangements | integer | The count of unique rearrangements identified in the sample. Each rearrangement may be present in multiple cells. A rearrangement is a particular nucleotide sequence generated through V(D)J recombination. |
| Productive Rearrangements | productive_rearrangements | integer | The count of unique rearrangements in the sample that are in-frame and do not contain a stop codon. Productive rearrangements can produce a functional protein receptor. |
| Productive Simpson Clonality | productive_simpson_clonality | double | Productive Simpson Clonality is calculated for a sample as the square root of Simpson’s diversity index for all productive rearrangements. Values for clonality range from 0 to 1. Values near 1 represent samples with one or a few predominant rearrangements (monoclonal or oligoclonal samples) dominating the observed repertoire. Clonality values near 0 represent more polyclonal samples. |
| Fraction T Cells of Nucleated Cells | fraction_productive_of_cells | fraction (0.0 – 1.0) | The fraction of T cells within the total nucleated cell count (T cells and non-T cells). This value is calculated by dividing the number of Productive Templates by Nucleated Cells. |
| Max Productive Frequency | max_productive_frequency | fraction (0.0 – 1.0) | The maximum Productive Frequency value found within a sample. Productive Frequency for a specific productive rearrangement is calculated as the Templates for a specific rearrangement divided by the Sum of Productive Templates for a sample. |
| HLA Class I | hla_class_i | csv | The HLA Class I type metadata provided by the customer upon receipt of specimen; usually presented as a comma-delimited string of Class I alleles, e.g. “A*02:01,A*23:01,B*40:02...” |
| HLA Class II | hla_class_ii | csv | The HLA Class II type metadata provided by the customer upon receipt of specimen; usually presented as a comma-delimited string of Class II alleles, e.g. “DPA1*02:02,DPA1*02:02,DPB1*...” |
| Sample Tags | sample_tags | csv | The metadata tags associated with this sample. Sample tags are either from the Adaptive Tag Library, or project-specific tags defined and created by the sample owner* |