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FHIR IG Statistics: StructureDefinition/ext-R3-Sequence.variant

Packagehl7.fhir.uv.xver-r3.r5
Resource TypeStructureDefinition
Idext-R3-Sequence.variant
FHIR VersionR5
Sourcehttp://hl7.org/fhir/uv/xver/https://simplifier.net/resolve?scope=hl7.fhir.uv.xver-r3.r5@0.0.1-snapshot-1&canonical=http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant
URLhttp://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant
Version0.0.1-snapshot-1
Statusdraft
Date2025-06-03T03:12:25.2345073+02:00
Nameext_R3_Sequence_variant
TitleCross-version Extension for R3.Sequence.variant for use in FHIR R5
Realmuv
Authorityhl7
DescriptionThis cross-version extension represents Sequence.variant from http://hl7.org/fhir/StructureDefinition/Sequence|3.0.2 for use in FHIR R5.
TypeExtension
Kindcomplex-type

Resources that use this resource

No resources found


Resources that this resource uses

No resources found


Examples of Use for Extension

No extension usage examples found


Narrative

No narrative content found in resource


Source

{
  "resourceType": "StructureDefinition",
  "id": "ext-R3-Sequence.variant",
  "url": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant",
  "version": "0.0.1-snapshot-1",
  "name": "ext_R3_Sequence_variant",
  "title": "Cross-version Extension for R3.Sequence.variant for use in FHIR R5",
  "status": "draft",
  "experimental": false,
  "date": "2025-06-03T03:12:25.2345073+02:00",
  "description": "This cross-version extension represents Sequence.variant from http://hl7.org/fhir/StructureDefinition/Sequence|3.0.2 for use in FHIR R5.",
  "fhirVersion": "5.0.0",
  "kind": "complex-type",
  "abstract": false,
  "context": [
    {
      "type": "element",
      "expression": "MolecularSequence"
    }
  ],
  "type": "Extension",
  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",
  "derivation": "constraint",
  "snapshot": {
    "element": [
      {
        "id": "Extension",
        "path": "Extension",
        "short": "Variant in sequence",
        "definition": "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.)  It can represent some complex mutation or segment variation with the assist of CIGAR string.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "*",
        "base": {
          "path": "Extension",
          "min": 0,
          "max": "*"
        },
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a,N/A"
          }
        ]
      },
      {
        "id": "Extension.id",
        "path": "Extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension",
        "path": "Extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "ordered": false,
          "rules": "closed"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:start",
        "path": "Extension.extension",
        "sliceName": "start",
        "short": "Start position of the variant on the  reference sequence",
        "definition": "Start position of the variant on the  reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "alias": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:start.id",
        "path": "Extension.extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:start.extension",
        "path": "Extension.extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "rules": "open"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:start.url",
        "path": "Extension.extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "start",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:start.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Start position of the variant on the  reference sequence",
        "definition": "Start position of the variant on the  reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "integer"
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:end",
        "path": "Extension.extension",
        "sliceName": "end",
        "short": "End position of the variant on the reference sequence",
        "definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "alias": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:end.id",
        "path": "Extension.extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:end.extension",
        "path": "Extension.extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "rules": "open"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:end.url",
        "path": "Extension.extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "end",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:end.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "End position of the variant on the reference sequence",
        "definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "integer"
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:observedAllele",
        "path": "Extension.extension",
        "sliceName": "observedAllele",
        "short": "Allele that was observed",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).  Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed  sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "alias": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:observedAllele.id",
        "path": "Extension.extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:observedAllele.extension",
        "path": "Extension.extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "rules": "open"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:observedAllele.url",
        "path": "Extension.extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "observedAllele",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:observedAllele.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Allele that was observed",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).  Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed  sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "string"
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:referenceAllele",
        "path": "Extension.extension",
        "sliceName": "referenceAllele",
        "short": "Allele in the reference sequence",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "alias": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:referenceAllele.id",
        "path": "Extension.extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:referenceAllele.extension",
        "path": "Extension.extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "rules": "open"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:referenceAllele.url",
        "path": "Extension.extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "referenceAllele",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:referenceAllele.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Allele in the reference sequence",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "string"
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:cigar",
        "path": "Extension.extension",
        "sliceName": "cigar",
        "short": "Extended CIGAR string for aligning the sequence with reference bases",
        "definition": "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "alias": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:cigar.id",
        "path": "Extension.extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:cigar.extension",
        "path": "Extension.extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "rules": "open"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:cigar.url",
        "path": "Extension.extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "cigar",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:cigar.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Extended CIGAR string for aligning the sequence with reference bases",
        "definition": "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "string"
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:variantPointer",
        "path": "Extension.extension",
        "sliceName": "variantPointer",
        "short": "Pointer to observed variant information",
        "definition": "A pointer to an Observation containing variant information.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "alias": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:variantPointer.id",
        "path": "Extension.extension.id",
        "representation": [
          "xmlAttr"
        ],
        "short": "Unique id for inter-element referencing",
        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Element.id",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "id"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "condition": [
          "ele-1"
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:variantPointer.extension",
        "path": "Extension.extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "description": "Extensions are always sliced by (at least) url",
          "rules": "open"
        },
        "short": "Additional content defined by implementations",
        "definition": "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 managable, 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": "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": [
          "extensions",
          "user content"
        ],
        "min": 0,
        "max": "*",
        "base": {
          "path": "Element.extension",
          "min": 0,
          "max": "*"
        },
        "type": [
          {
            "code": "Extension"
          }
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          },
          {
            "key": "ext-1",
            "severity": "error",
            "human": "Must have either extensions or value[x], not both",
            "expression": "extension.exists() != value.exists()",
            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "n/a"
          }
        ]
      },
      {
        "id": "Extension.extension:variantPointer.url",
        "path": "Extension.extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "variantPointer",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.extension:variantPointer.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Pointer to observed variant information",
        "definition": "A pointer to an Observation containing variant information.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "Reference",
            "targetProfile": [
              "http://hl7.org/fhir/StructureDefinition/Observation"
            ]
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.url",
        "path": "Extension.url",
        "representation": [
          "xmlAttr"
        ],
        "short": "identifies the meaning of the extension",
        "definition": "Source of the definition for the extension code - a logical name or a URL.",
        "comment": "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": 1,
        "max": "1",
        "base": {
          "path": "Extension.url",
          "min": 1,
          "max": "1"
        },
        "type": [
          {
            "extension": [
              {
                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
                "valueUrl": "uri"
              }
            ],
            "code": "http://hl7.org/fhirpath/System.String"
          }
        ],
        "fixedUri": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant",
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      },
      {
        "id": "Extension.value[x]",
        "path": "Extension.value[x]",
        "short": "Value of extension",
        "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](extensibility.html) for a list).",
        "min": 0,
        "max": "1",
        "base": {
          "path": "Extension.value[x]",
          "min": 0,
          "max": "1"
        },
        "type": [
          {
            "code": "base64Binary"
          },
          {
            "code": "boolean"
          },
          {
            "code": "canonical"
          },
          {
            "code": "code"
          },
          {
            "code": "date"
          },
          {
            "code": "dateTime"
          },
          {
            "code": "decimal"
          },
          {
            "code": "id"
          },
          {
            "code": "instant"
          },
          {
            "code": "integer"
          },
          {
            "code": "integer64"
          },
          {
            "code": "markdown"
          },
          {
            "code": "oid"
          },
          {
            "code": "positiveInt"
          },
          {
            "code": "string"
          },
          {
            "code": "time"
          },
          {
            "code": "unsignedInt"
          },
          {
            "code": "uri"
          },
          {
            "code": "url"
          },
          {
            "code": "uuid"
          },
          {
            "code": "Address"
          },
          {
            "code": "Age"
          },
          {
            "code": "Annotation"
          },
          {
            "code": "Attachment"
          },
          {
            "code": "CodeableConcept"
          },
          {
            "code": "CodeableReference"
          },
          {
            "code": "Coding"
          },
          {
            "code": "ContactPoint"
          },
          {
            "code": "Count"
          },
          {
            "code": "Distance"
          },
          {
            "code": "Duration"
          },
          {
            "code": "HumanName"
          },
          {
            "code": "Identifier"
          },
          {
            "code": "Money"
          },
          {
            "code": "Period"
          },
          {
            "code": "Quantity"
          },
          {
            "code": "Range"
          },
          {
            "code": "Ratio"
          },
          {
            "code": "RatioRange"
          },
          {
            "code": "Reference"
          },
          {
            "code": "SampledData"
          },
          {
            "code": "Signature"
          },
          {
            "code": "Timing"
          },
          {
            "code": "ContactDetail"
          },
          {
            "code": "DataRequirement"
          },
          {
            "code": "Expression"
          },
          {
            "code": "ParameterDefinition"
          },
          {
            "code": "RelatedArtifact"
          },
          {
            "code": "TriggerDefinition"
          },
          {
            "code": "UsageContext"
          },
          {
            "code": "Availability"
          },
          {
            "code": "ExtendedContactDetail"
          },
          {
            "code": "Dosage"
          },
          {
            "code": "Meta"
          }
        ],
        "condition": [
          "ext-1"
        ],
        "constraint": [
          {
            "key": "ele-1",
            "severity": "error",
            "human": "All FHIR elements must have a @value or children",
            "expression": "hasValue() or (children().count() > id.count())",
            "source": "http://hl7.org/fhir/StructureDefinition/Element"
          }
        ],
        "isModifier": false,
        "isSummary": false,
        "mapping": [
          {
            "identity": "rim",
            "map": "N/A"
          }
        ]
      }
    ]
  },
  "differential": {
    "element": [
      {
        "id": "Extension",
        "path": "Extension",
        "short": "Variant in sequence",
        "definition": "The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.)  It can represent some complex mutation or segment variation with the assist of CIGAR string.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "*",
        "isModifier": false
      },
      {
        "id": "Extension.extension",
        "path": "Extension.extension",
        "slicing": {
          "discriminator": [
            {
              "type": "value",
              "path": "url"
            }
          ],
          "ordered": false,
          "rules": "closed"
        },
        "min": 0,
        "max": "*"
      },
      {
        "id": "Extension.extension:start",
        "path": "Extension.extension",
        "sliceName": "start",
        "short": "Start position of the variant on the  reference sequence",
        "definition": "Start position of the variant on the  reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "isModifier": false
      },
      {
        "id": "Extension.extension:start.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Start position of the variant on the  reference sequence",
        "definition": "Start position of the variant on the  reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "base": {
          "path": "Extension.value[x]"
        },
        "type": [
          {
            "code": "integer"
          }
        ]
      },
      {
        "id": "Extension.extension:end",
        "path": "Extension.extension",
        "sliceName": "end",
        "short": "End position of the variant on the reference sequence",
        "definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "isModifier": false
      },
      {
        "id": "Extension.extension:end.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "End position of the variant on the reference sequence",
        "definition": "End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "base": {
          "path": "Extension.value[x]"
        },
        "type": [
          {
            "code": "integer"
          }
        ]
      },
      {
        "id": "Extension.extension:observedAllele",
        "path": "Extension.extension",
        "sliceName": "observedAllele",
        "short": "Allele that was observed",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).  Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed  sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "isModifier": false
      },
      {
        "id": "Extension.extension:observedAllele.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Allele that was observed",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)).  Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed  sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "base": {
          "path": "Extension.value[x]"
        },
        "type": [
          {
            "code": "string"
          }
        ]
      },
      {
        "id": "Extension.extension:referenceAllele",
        "path": "Extension.extension",
        "sliceName": "referenceAllele",
        "short": "Allele in the reference sequence",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "isModifier": false
      },
      {
        "id": "Extension.extension:referenceAllele.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Allele in the reference sequence",
        "definition": "An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence  type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "base": {
          "path": "Extension.value[x]"
        },
        "type": [
          {
            "code": "string"
          }
        ]
      },
      {
        "id": "Extension.extension:cigar",
        "path": "Extension.extension",
        "sliceName": "cigar",
        "short": "Extended CIGAR string for aligning the sequence with reference bases",
        "definition": "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "isModifier": false
      },
      {
        "id": "Extension.extension:cigar.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Extended CIGAR string for aligning the sequence with reference bases",
        "definition": "Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm).",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "base": {
          "path": "Extension.value[x]"
        },
        "type": [
          {
            "code": "string"
          }
        ]
      },
      {
        "id": "Extension.extension:variantPointer",
        "path": "Extension.extension",
        "sliceName": "variantPointer",
        "short": "Pointer to observed variant information",
        "definition": "A pointer to an Observation containing variant information.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "min": 0,
        "max": "1",
        "isModifier": false
      },
      {
        "id": "Extension.extension:variantPointer.value[x]",
        "path": "Extension.extension.value[x]",
        "short": "Pointer to observed variant information",
        "definition": "A pointer to an Observation containing variant information.",
        "comment": "`MolecularSequence.variant` has no related element in R5:MolecularSequence",
        "base": {
          "path": "Extension.value[x]"
        },
        "type": [
          {
            "code": "Reference",
            "targetProfile": [
              "http://hl7.org/fhir/StructureDefinition/Observation"
            ]
          }
        ]
      },
      {
        "id": "Extension.url",
        "path": "Extension.url",
        "min": 1,
        "max": "1",
        "fixedUri": "http://hl7.org/fhir/3.0/StructureDefinition/extension-Sequence.variant"
      }
    ]
  }
}