Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
| Active as of 2024-12-12 |
XML representation of the genomic-study-analysis-metrics extension.
<StructureDefinition xmlns="http://hl7.org/fhir">
<id value="genomic-study-analysis-metrics"/>
<text>
<status value="extensions"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: StructureDefinition genomic-study-analysis-metrics</b></p><a name="genomic-study-analysis-metrics"> </a><a name="hcgenomic-study-analysis-metrics"> </a><a name="genomic-study-analysis-metrics-en-US"> </a><table border="0" cellpadding="0" cellspacing="0" style="border: 0px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top;"><tr style="border: 1px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top"><th style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="The logical name of the element">Name</a></th><th style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Information about the use of the element">Flags</a></th><th style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Minimum and Maximum # of times the element can appear in the instance">Card.</a></th><th style="width: 100px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Reference to the type of the element">Type</a></th><th style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Additional information about the element">Description & Constraints</a><span style="float: right"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Legend for this format"><img src="data:image/png;base64,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" alt="doco" style="background-color: inherit"/></a></span></th></tr><tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension" title="Metrics about the sequencing analysis that was performed">Extension</a><a name="Extension"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">0</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">*</span></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">Genomic Study Analysis Metrics</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck13.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Slice Definition" class="hierarchy"/> Slices for extension<a name="Extension.extension"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">Content/Rules for all slices</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck135.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:read-depth" title="Slice read-depth: The average read depth (number of reads for a position) for the sequencing test">extension:read-depth</a><a name="Extension.extension.2"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">Read Depth</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Simple Extension" class="hierarchy"/> <span style="text-decoration:line-through">extension</span><a name="Extension.extension.extension"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="text-decoration:line-through"/><span style="text-decoration:line-through">0</span><span style="text-decoration:line-through">..</span><span style="text-decoration:line-through">0</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:read-depth.url">url</a><a name="Extension.extension.url"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">1</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/datatypes.html#uri">uri</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="color: darkgreen">"read-depth"</span></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1340.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_datatype.gif" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Data Type" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:read-depth.value[x]">value[x]</a><a name="Extension.extension.value_x_"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">0</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#SimpleQuantity" title="Quantity">SimpleQuantity</a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">30, 100</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck135.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:sequencing-coverage" title="Slice sequencing-coverage: The percentage of the studied regions that were sequenced">extension:sequencing-coverage</a><a name="Extension.extension.3"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">Sequencing Coverage</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Simple Extension" class="hierarchy"/> <span style="text-decoration:line-through">extension</span><a name="Extension.extension.extension.2"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="text-decoration:line-through"/><span style="text-decoration:line-through">0</span><span style="text-decoration:line-through">..</span><span style="text-decoration:line-through">0</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1350.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:sequencing-coverage.url">url</a><a name="Extension.extension.url.2"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">1</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/datatypes.html#uri">uri</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="color: darkgreen">"sequencing-coverage"</span></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1340.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_datatype.gif" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Data Type" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:sequencing-coverage.value[x]">value[x]</a><a name="Extension.extension.value_x_.2"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">0</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#SimpleQuantity" title="Quantity">SimpleQuantity</a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">95, 100</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck125.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:metrics-description" title="Slice metrics-description: Freetext description of the coverage metrics for the sequencing test">extension:metrics-description</a><a name="Extension.extension.4"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">Metrics Description</td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1250.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Simple Extension" class="hierarchy"/> <span style="text-decoration:line-through">extension</span><a name="Extension.extension.extension.3"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="text-decoration:line-through"/><span style="text-decoration:line-through">0</span><span style="text-decoration:line-through">..</span><span style="text-decoration:line-through">0</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1250.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:metrics-description.url">url</a><a name="Extension.extension.url.3"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">1</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/datatypes.html#uri">uri</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="color: darkgreen">"metrics-description"</span></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1240.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slice.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_primitive.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Primitive Data Type" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.extension:metrics-description.value[x]">value[x]</a><a name="Extension.extension.value_x_.3"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">0</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#string">string</a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Value of extension</span></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck10.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-genomic-study-analysis-metrics-definitions.html#Extension.url">url</a><a name="Extension.url"> </a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">1</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">1</span></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5" href="http://hl7.org/fhir/R4/datatypes.html#uri">uri</a></td><td style="vertical-align: top; text-align : left; background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="color: darkgreen">"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"</span></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck00.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Element" class="hierarchy"/> <span style="text-decoration:line-through">value[x]</span><a name="Extension.value_x_"> </a></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="text-decoration:line-through"/><span style="text-decoration:line-through">0</span><span style="text-decoration:line-through">..</span><span style="text-decoration:line-through">0</span></td><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : left; background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr><td colspan="5" class="hierarchy"><br/><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Legend for this format"><img src="data:image/png;base64,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" alt="doco" style="background-color: inherit"/> Documentation for this format</a></td></tr></table></div>
</text>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
<valueCode value="cg"/>
</extension>
<url
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"/>
<version value="3.0.0"/>
<name value="GenomicStudyAnalysisMetrics"/>
<title value="Genomic Study Analysis Metrics"/>
<status value="active"/>
<date value="2024-12-12T20:43:36+00:00"/>
<publisher value="HL7 International / Clinical Genomics"/>
<contact>
<name value="HL7 International / Clinical Genomics"/>
<telecom>
<system value="url"/>
<value value="http://www.hl7.org/Special/committees/clingenomics"/>
</telecom>
<telecom>
<system value="email"/>
<value value="cg@lists.HL7.org"/>
</telecom>
</contact>
<description
value="Metrics about the sequencing analysis that was performed"/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
<display value="World"/>
</coding>
</jurisdiction>
<fhirVersion value="4.0.1"/>
<mapping>
<identity value="rim"/>
<uri value="http://hl7.org/v3"/>
<name value="RIM Mapping"/>
</mapping>
<kind value="complex-type"/>
<abstract value="false"/>
<context>
<type value="element"/>
<expression value="Procedure"/>
</context>
<type value="Extension"/>
<baseDefinition value="http://hl7.org/fhir/StructureDefinition/Extension"/>
<derivation value="constraint"/>
<snapshot>
<element id="Extension">
<path value="Extension"/>
<short value="Genomic Study Analysis Metrics"/>
<definition
value="Metrics about the sequencing analysis that was performed"/>
<min value="0"/>
<max value="*"/>
<base>
<path value="Extension"/>
<min value="0"/>
<max value="*"/>
</base>
<condition value="ele-1"/>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
</element>
<element id="Extension.id">
<path value="Extension.id"/>
<representation value="xmlAttr"/>
<short value="Unique id for inter-element referencing"/>
<definition
value="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.id"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="string"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="Extension.extension">
<path value="Extension.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<description value="Extensions are always sliced by (at least) url"/>
<rules value="open"/>
</slicing>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."/>
<comment
value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
<alias value="extensions"/>
<alias value="user content"/>
<min value="0"/>
<max value="*"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="Extension.extension:read-depth">
<path value="Extension.extension"/>
<sliceName value="read-depth"/>
<short value="Read Depth"/>
<definition
value="The average read depth (number of reads for a position) for the sequencing test"/>
<requirements
value="This value is typically represented with an 'x' after the number (30x). Simply share the quantity here."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="Extension.extension:read-depth.id">
<path value="Extension.extension.id"/>
<representation value="xmlAttr"/>
<short value="Unique id for inter-element referencing"/>
<definition
value="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.id"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="string"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="Extension.extension:read-depth.extension">
<path value="Extension.extension.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<description value="Extensions are always sliced by (at least) url"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="0"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="Extension.extension:read-depth.url">
<path value="Extension.extension.url"/>
<representation value="xmlAttr"/>
<short value="identifies the meaning of the extension"/>
<definition
value="Source of the definition for the extension code - a logical name or a URL."/>
<comment
value="The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="Extension.url"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="uri"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<fixedUri value="read-depth"/>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="Extension.extension:read-depth.value[x]">
<path value="Extension.extension.value[x]"/>
<short value="30, 100"/>
<definition value="The comparator is not used on a SimpleQuantity"/>
<comment
value="The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Extension.value[x]"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Quantity"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity"/>
</type>
<condition value="ele-1"/>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="qty-3"/>
<severity value="error"/>
<human
value="If a code for the unit is present, the system SHALL also be present"/>
<expression value="code.empty() or system.exists()"/>
<xpath value="not(exists(f:code)) or exists(f:system)"/>
<source value="http://hl7.org/fhir/StructureDefinition/Quantity"/>
</constraint>
<constraint>
<key value="sqty-1"/>
<severity value="error"/>
<human value="The comparator is not used on a SimpleQuantity"/>
<expression value="comparator.empty()"/>
<xpath value="not(exists(f:comparator))"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
<mapping>
<identity value="v2"/>
<map value="SN (see also Range) or CQ"/>
</mapping>
<mapping>
<identity value="rim"/>
<map value="PQ, IVL<PQ>, MO, CO, depending on the values"/>
</mapping>
</element>
<element id="Extension.extension:sequencing-coverage">
<path value="Extension.extension"/>
<sliceName value="sequencing-coverage"/>
<short value="Sequencing Coverage"/>
<definition
value="The percentage of the studied regions that were sequenced"/>
<requirements
value="This value is typically represented with an '%' after the number (95%). Simply share the quantity here."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="Extension.extension:sequencing-coverage.id">
<path value="Extension.extension.id"/>
<representation value="xmlAttr"/>
<short value="Unique id for inter-element referencing"/>
<definition
value="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.id"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="string"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="Extension.extension:sequencing-coverage.extension">
<path value="Extension.extension.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<description value="Extensions are always sliced by (at least) url"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="0"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="Extension.extension:sequencing-coverage.url">
<path value="Extension.extension.url"/>
<representation value="xmlAttr"/>
<short value="identifies the meaning of the extension"/>
<definition
value="Source of the definition for the extension code - a logical name or a URL."/>
<comment
value="The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="Extension.url"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="uri"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<fixedUri value="sequencing-coverage"/>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="Extension.extension:sequencing-coverage.value[x]">
<path value="Extension.extension.value[x]"/>
<short value="95, 100"/>
<definition value="The comparator is not used on a SimpleQuantity"/>
<comment
value="The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Extension.value[x]"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Quantity"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity"/>
</type>
<condition value="ele-1"/>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="qty-3"/>
<severity value="error"/>
<human
value="If a code for the unit is present, the system SHALL also be present"/>
<expression value="code.empty() or system.exists()"/>
<xpath value="not(exists(f:code)) or exists(f:system)"/>
<source value="http://hl7.org/fhir/StructureDefinition/Quantity"/>
</constraint>
<constraint>
<key value="sqty-1"/>
<severity value="error"/>
<human value="The comparator is not used on a SimpleQuantity"/>
<expression value="comparator.empty()"/>
<xpath value="not(exists(f:comparator))"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
<mapping>
<identity value="v2"/>
<map value="SN (see also Range) or CQ"/>
</mapping>
<mapping>
<identity value="rim"/>
<map value="PQ, IVL<PQ>, MO, CO, depending on the values"/>
</mapping>
</element>
<element id="Extension.extension:metrics-description">
<path value="Extension.extension"/>
<sliceName value="metrics-description"/>
<short value="Metrics Description"/>
<definition
value="Freetext description of the coverage metrics for the sequencing test"/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="Extension.extension:metrics-description.id">
<path value="Extension.extension.id"/>
<representation value="xmlAttr"/>
<short value="Unique id for inter-element referencing"/>
<definition
value="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.id"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="string"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="Extension.extension:metrics-description.extension">
<path value="Extension.extension.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<description value="Extensions are always sliced by (at least) url"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="0"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<constraint>
<key value="ext-1"/>
<severity value="error"/>
<human value="Must have either extensions or value[x], not both"/>
<expression value="extension.exists() != value.exists()"/>
<xpath
value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")])"/>
<source value="http://hl7.org/fhir/StructureDefinition/Extension"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="Extension.extension:metrics-description.url">
<path value="Extension.extension.url"/>
<representation value="xmlAttr"/>
<short value="identifies the meaning of the extension"/>
<definition
value="Source of the definition for the extension code - a logical name or a URL."/>
<comment
value="The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="Extension.url"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="uri"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<fixedUri value="metrics-description"/>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="Extension.extension:metrics-description.value[x]">
<path value="Extension.extension.value[x]"/>
<short value="Value of extension"/>
<definition
value="Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Extension.value[x]"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="Extension.url">
<path value="Extension.url"/>
<representation value="xmlAttr"/>
<short value="identifies the meaning of the extension"/>
<definition
value="Source of the definition for the extension code - a logical name or a URL."/>
<comment
value="The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="Extension.url"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type">
<valueUrl value="uri"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<fixedUri
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"/>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="Extension.value[x]">
<path value="Extension.value[x]"/>
<short value="Value of extension"/>
<definition
value="Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/R4/extensibility.html) for a list)."/>
<min value="0"/>
<max value="0"/>
<base>
<path value="Extension.value[x]"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="base64Binary"/>
</type>
<type>
<code value="boolean"/>
</type>
<type>
<code value="canonical"/>
</type>
<type>
<code value="code"/>
</type>
<type>
<code value="date"/>
</type>
<type>
<code value="dateTime"/>
</type>
<type>
<code value="decimal"/>
</type>
<type>
<code value="id"/>
</type>
<type>
<code value="instant"/>
</type>
<type>
<code value="integer"/>
</type>
<type>
<code value="markdown"/>
</type>
<type>
<code value="oid"/>
</type>
<type>
<code value="positiveInt"/>
</type>
<type>
<code value="string"/>
</type>
<type>
<code value="time"/>
</type>
<type>
<code value="unsignedInt"/>
</type>
<type>
<code value="uri"/>
</type>
<type>
<code value="url"/>
</type>
<type>
<code value="uuid"/>
</type>
<type>
<code value="Address"/>
</type>
<type>
<code value="Age"/>
</type>
<type>
<code value="Annotation"/>
</type>
<type>
<code value="Attachment"/>
</type>
<type>
<code value="CodeableConcept"/>
</type>
<type>
<code value="Coding"/>
</type>
<type>
<code value="ContactPoint"/>
</type>
<type>
<code value="Count"/>
</type>
<type>
<code value="Distance"/>
</type>
<type>
<code value="Duration"/>
</type>
<type>
<code value="HumanName"/>
</type>
<type>
<code value="Identifier"/>
</type>
<type>
<code value="Money"/>
</type>
<type>
<code value="Period"/>
</type>
<type>
<code value="Quantity"/>
</type>
<type>
<code value="Range"/>
</type>
<type>
<code value="Ratio"/>
</type>
<type>
<code value="Reference"/>
</type>
<type>
<code value="SampledData"/>
</type>
<type>
<code value="Signature"/>
</type>
<type>
<code value="Timing"/>
</type>
<type>
<code value="ContactDetail"/>
</type>
<type>
<code value="Contributor"/>
</type>
<type>
<code value="DataRequirement"/>
</type>
<type>
<code value="Expression"/>
</type>
<type>
<code value="ParameterDefinition"/>
</type>
<type>
<code value="RelatedArtifact"/>
</type>
<type>
<code value="TriggerDefinition"/>
</type>
<type>
<code value="UsageContext"/>
</type>
<type>
<code value="Dosage"/>
</type>
<type>
<code value="Meta"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source value="http://hl7.org/fhir/StructureDefinition/Element"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
</snapshot>
<differential>
<element id="Extension">
<path value="Extension"/>
<short value="Genomic Study Analysis Metrics"/>
<definition
value="Metrics about the sequencing analysis that was performed"/>
</element>
<element id="Extension.extension:read-depth">
<path value="Extension.extension"/>
<sliceName value="read-depth"/>
<short value="Read Depth"/>
<definition
value="The average read depth (number of reads for a position) for the sequencing test"/>
<requirements
value="This value is typically represented with an 'x' after the number (30x). Simply share the quantity here."/>
<min value="0"/>
<max value="1"/>
</element>
<element id="Extension.extension:read-depth.extension">
<path value="Extension.extension.extension"/>
<max value="0"/>
</element>
<element id="Extension.extension:read-depth.url">
<path value="Extension.extension.url"/>
<fixedUri value="read-depth"/>
</element>
<element id="Extension.extension:read-depth.value[x]">
<path value="Extension.extension.value[x]"/>
<short value="30, 100"/>
<type>
<code value="Quantity"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity"/>
</type>
</element>
<element id="Extension.extension:sequencing-coverage">
<path value="Extension.extension"/>
<sliceName value="sequencing-coverage"/>
<short value="Sequencing Coverage"/>
<definition
value="The percentage of the studied regions that were sequenced"/>
<requirements
value="This value is typically represented with an '%' after the number (95%). Simply share the quantity here."/>
<min value="0"/>
<max value="1"/>
</element>
<element id="Extension.extension:sequencing-coverage.extension">
<path value="Extension.extension.extension"/>
<max value="0"/>
</element>
<element id="Extension.extension:sequencing-coverage.url">
<path value="Extension.extension.url"/>
<fixedUri value="sequencing-coverage"/>
</element>
<element id="Extension.extension:sequencing-coverage.value[x]">
<path value="Extension.extension.value[x]"/>
<short value="95, 100"/>
<type>
<code value="Quantity"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/SimpleQuantity"/>
</type>
</element>
<element id="Extension.extension:metrics-description">
<path value="Extension.extension"/>
<sliceName value="metrics-description"/>
<short value="Metrics Description"/>
<definition
value="Freetext description of the coverage metrics for the sequencing test"/>
<min value="0"/>
<max value="1"/>
</element>
<element id="Extension.extension:metrics-description.extension">
<path value="Extension.extension.extension"/>
<max value="0"/>
</element>
<element id="Extension.extension:metrics-description.url">
<path value="Extension.extension.url"/>
<fixedUri value="metrics-description"/>
</element>
<element id="Extension.extension:metrics-description.value[x]">
<path value="Extension.extension.value[x]"/>
<type>
<code value="string"/>
</type>
</element>
<element id="Extension.url">
<path value="Extension.url"/>
<fixedUri
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"/>
</element>
<element id="Extension.value[x]">
<path value="Extension.value[x]"/>
<max value="0"/>
</element>
</differential>
</StructureDefinition>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change