QC Contextual Data Tags Specification.csv

Field;Definition;Ontology ID;Data Type;Values;Example
quality_control_method_name;The name of the method used to assess whether a sequence passed a predetermined quality control threshold.;GENEPIO:0100557;String;No prescribed values;ncov-tools
quality_control_method_version;The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.;GENEPIO:0100558;String;No prescribed values;1.2.3
quality_control_determination;The determination of a quality control assessment.;GENEPIO:0100559;Enums;"no quality control issues identified [GENEPIO:0100562]; sequence passed quality control [GENEPIO:0100563]; sequence failed quality control [GENEPIO:0100564]; minor quality control issues identified [GENEPIO:0100565]; sequence flagged for potential quality control issues [GENEPIO:0100566]; quality control not performed [GENEPIO:0100567]";sequence failed quality control [GENEPIO:0100564]
quality_control_issues;The reason contributing to, or causing, a low quality determination in a quality control assessment.;GENEPIO:0100560;Enums;"low quality sequence [GENEPIO:0100568]; sequenced contaminated [GENEPIO:0100569]; low average genome coverage [GENEPIO:0100570]; low percent genome captured [GENEPIO:0100571]; read lengths shorter than expected [GENEPIO:0100572]; sequence amplification artifacts [GENEPIO:0100573]; low signal to noise ratio [GENEPIO:0100574]; low coverage of characteristic mutations [GENEPIO:0100575]"; excess frameshift mutations detected [GENEPIO:0100751]; low average genome coverage [GENEPIO:0100570]
quality_control_details;The details surrounding a low quality determination in a quality control assessment.;GENEPIO:0100561;String;none;CT value of 39. Low viral load. Low DNA concentration after amplification.