Looker report
The Looker report is intended for use in Google's Looker Studio Data Studio for dashboarding purposes. It offers a highly condensed version of the resistance calls (using the looker_interpretation field from the laboratorian report) for a quick summary of the sample’s drug resistance profile.
Explanation of column headers¶
| Column name | Explanation |
|---|---|
| sample_id | The name of the sample |
| output_seq_method_type | The sequencing method used to generate the data; can be set with the --sequencing_method input parameter. If left blank, “Sequencing method not provided” is the default value |
| amikacin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| bedaquiline | The highest looker_interpretation resistance identified for mutations associated with this drug |
| capreomycin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| clofazimine | The highest looker_interpretation resistance identified for mutations associated with this drug |
| ethambutol | The highest looker_interpretation resistance identified for mutations associated with this drug |
| ethionamide | The highest looker_interpretation resistance identified for mutations associated with this drug |
| isoniazid | The highest looker_interpretation resistance identified for mutations associated with this drug |
| kanamycin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| levofloxacin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| linezolid | The highest looker_interpretation resistance identified for mutations associated with this drug |
| moxifloxacin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| pyrazinamide | The highest looker_interpretation resistance identified for mutations associated with this drug |
| rifampin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| streptomycin | The highest looker_interpretation resistance identified for mutations associated with this drug |
| lineage | The lineage of the sample (the main_lin field as reported by TB-Profiler); for example, lineage1.2.1.2.1 |
| ID | The lineage of the sample in human-readable language (the same as M_DST_A01_ID in the LIMS report) |
| analysis_date | The date tbp-parser was run in YYYY-MM-DD HH:SS format |
| operator | The name of the person who ran tbp-parser; can be provided with the --operator input parameter. If left blank, “Operator not provided” is the default value. |
Please note that occasionally, the looker_interpretation field can differ from the mdl_interpretation field. Typically, they are identical, but occasionally, the mdl_interpretation column will call a variant-drug combination “susceptible” (S), while the looker_interpretation column will call the same combination “uncertain” (U). Be aware of this difference when choosing an interpretation to report.