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Return the results of a panel as JSON. The returned JSON has the following top-level structure:
PropertyDescription
panel_name stringThe name of the panel, e.g,. “Antibiotic Resistance Determinants” for the ARDM panel.
panel_results objectAn object consisting of 1 or more “sub-panels”, which then include the individual results for the markers (format below).
The panel_results object itself contains 1 or more sub-panels which consist of a description entry and then a list of markers. The markers themselves contain the following fields. Note that currently panels can consist of short and/or long markers, for which slightly different fields may be reported:
PropertyDescription
name stringThe name of the marker sequence.
description stringA description of the marker.
status stringWhether the marker sequence is ‘present’, ‘probable’, or ‘absent’. This determination is based on the below fields, but cutoff values may differ between panels. The default thresholds are as following: (1) for long markers identity and coverage >= 99% for “present” and >= 95% for “probable”; (2) for short markers the presence of an exact match is required for a “present” call and a partial match (<= 3 SNPs) is required for a “probable” call.
length integerThe length of the marker sequence.
identity numberThe percent identity of the detected marker sequence in the sample. Provided only for “long” marker sequences (e.g., genes).
coverage numberThe coverage of the detected marker sequence in the sample. Provided only for “long” marker sequences (e.g., genes).
depth numberThe depth of coverage for the detected marker sequence in the sample. Provided only for “long” marker sequences (e.g., genes).
n_reads_exact_match integerThe number of reads including an exact match to the marker sequence. Provided only for “short” marker sequences (e.g., <= ~50 bp).
n_reads_partial_match integerThe number of reads including an partial match to the marker sequence. By default, a partial match is defined as being within 3 SNPs of the exact sequence. Provided only for “short” marker sequences (e.g., <= ~50 bp).
Warning: The above JSON format is not guaranteed to remain stable, though we do not expect to substantively alter the meaning of any fields. Please use caution and include fallbacks when writing non-exploratory code using the above route. Please also feel free to reach out if you’d like to discuss this format and any forthcoming changes with us.