Property | Description |
---|---|
panel_name string | The name of the panel, e.g,. “Antibiotic Resistance Determinants” for the ARDM panel. |
panel_results object | An object consisting of 1 or more “sub-panels”, which then include the individual results for the markers (format below). |
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:
Property | Description |
---|---|
name string | The name of the marker sequence. |
description string | A description of the marker. |
status string | Whether 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 integer | The length of the marker sequence. |
identity number | The percent identity of the detected marker sequence in the sample. Provided only for “long” marker sequences (e.g., genes). |
coverage number | The coverage of the detected marker sequence in the sample. Provided only for “long” marker sequences (e.g., genes). |
depth number | The depth of coverage for the detected marker sequence in the sample. Provided only for “long” marker sequences (e.g., genes). |
n_reads_exact_match integer | The 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 integer | The 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 ). |
Successful operation
The response is of type object
.