@medplum/fhirtypes 0.3.0

package/dist/MolecularSequence.d.ts

@@ -0,0 +1,875 @@
+/*
+ * Generated by @medplum/generator
+ * Do not edit manually.
+ */
+
+import { CodeableConcept } from './CodeableConcept';
+import { Device } from './Device';
+import { Extension } from './Extension';
+import { Identifier } from './Identifier';
+import { Meta } from './Meta';
+import { Narrative } from './Narrative';
+import { Observation } from './Observation';
+import { Organization } from './Organization';
+import { Patient } from './Patient';
+import { Quantity } from './Quantity';
+import { Reference } from './Reference';
+import { Resource } from './Resource';
+import { Specimen } from './Specimen';
+
+/**
+ * Raw data describing a biological sequence.
+ */
+export interface MolecularSequence {
+
+  /**
+   * This is a MolecularSequence resource
+   */
+  readonly resourceType: 'MolecularSequence';
+
+  /**
+   * The logical id of the resource, as used in the URL for the resource.
+   * Once assigned, this value never changes.
+   */
+  readonly id?: string;
+
+  /**
+   * The metadata about the resource. This is content that is maintained by
+   * the infrastructure. Changes to the content might not always be
+   * associated with version changes to the resource.
+   */
+  readonly meta?: Meta;
+
+  /**
+   * A reference to a set of rules that were followed when the resource was
+   * constructed, and which must be understood when processing the content.
+   * Often, this is a reference to an implementation guide that defines the
+   * special rules along with other profiles etc.
+   */
+  readonly implicitRules?: string;
+
+  /**
+   * The base language in which the resource is written.
+   */
+  readonly language?: string;
+
+  /**
+   * A human-readable narrative that contains a summary of the resource and
+   * can be used to represent the content of the resource to a human. The
+   * narrative need not encode all the structured data, but is required to
+   * contain sufficient detail to make it "clinically safe" for a human to
+   * just read the narrative. Resource definitions may define what content
+   * should be represented in the narrative to ensure clinical safety.
+   */
+  readonly text?: Narrative;
+
+  /**
+   * These resources do not have an independent existence apart from the
+   * resource that contains them - they cannot be identified independently,
+   * and nor can they have their own independent transaction scope.
+   */
+  readonly contained?: Resource[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the resource. 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the resource and that modifies the
+   * understanding of the element that contains it and/or the understanding
+   * of the containing element's descendants. Usually modifier elements
+   * provide negation or qualification. 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 is allowed to
+   * define an extension, there is a set of requirements that SHALL be met
+   * as part of the definition of the extension. Applications processing a
+   * resource are required to check for modifier extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * A unique identifier for this particular sequence instance. This is a
+   * FHIR-defined id.
+   */
+  readonly identifier?: Identifier[];
+
+  /**
+   * Amino Acid Sequence/ DNA Sequence / RNA Sequence.
+   */
+  readonly type?: string;
+
+  /**
+   * Whether the sequence is numbered starting at 0 (0-based numbering or
+   * coordinates, inclusive start, exclusive end) or starting at 1 (1-based
+   * numbering, inclusive start and inclusive end).
+   */
+  readonly coordinateSystem?: number;
+
+  /**
+   * The patient whose sequencing results are described by this resource.
+   */
+  readonly patient?: Reference<Patient>;
+
+  /**
+   * Specimen used for sequencing.
+   */
+  readonly specimen?: Reference<Specimen>;
+
+  /**
+   * The method for sequencing, for example, chip information.
+   */
+  readonly device?: Reference<Device>;
+
+  /**
+   * The organization or lab that should be responsible for this result.
+   */
+  readonly performer?: Reference<Organization>;
+
+  /**
+   * The number of copies of the sequence of interest. (RNASeq).
+   */
+  readonly quantity?: Quantity;
+
+  /**
+   * A sequence that is used as a reference to describe variants that are
+   * present in a sequence analyzed.
+   */
+  readonly referenceSeq?: MolecularSequenceReferenceSeq;
+
+  /**
+   * 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.
+   */
+  readonly variant?: MolecularSequenceVariant[];
+
+  /**
+   * Sequence that was observed. It is the result marked by referenceSeq
+   * along with variant records on referenceSeq. This shall start from
+   * referenceSeq.windowStart and end by referenceSeq.windowEnd.
+   */
+  readonly observedSeq?: string;
+
+  /**
+   * An experimental feature attribute that defines the quality of the
+   * feature in a quantitative way, such as a phred quality score
+   * ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
+   */
+  readonly quality?: MolecularSequenceQuality[];
+
+  /**
+   * Coverage (read depth or depth) is the average number of reads
+   * representing a given nucleotide in the reconstructed sequence.
+   */
+  readonly readCoverage?: number;
+
+  /**
+   * Configurations of the external repository. The repository shall store
+   * target's observedSeq or records related with target's observedSeq.
+   */
+  readonly repository?: MolecularSequenceRepository[];
+
+  /**
+   * Pointer to next atomic sequence which at most contains one variant.
+   */
+  readonly pointer?: Reference<MolecularSequence>[];
+
+  /**
+   * Information about chromosome structure variation.
+   */
+  readonly structureVariant?: MolecularSequenceStructureVariant[];
+}
+
+/**
+ * An experimental feature attribute that defines the quality of the
+ * feature in a quantitative way, such as a phred quality score
+ * ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
+ */
+export interface MolecularSequenceQuality {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * INDEL / SNP / Undefined variant.
+   */
+  readonly type?: string;
+
+  /**
+   * Gold standard sequence used for comparing against.
+   */
+  readonly standardSequence?: CodeableConcept;
+
+  /**
+   * Start position of the sequence. If the coordinate system is either
+   * 0-based or 1-based, then start position is inclusive.
+   */
+  readonly start?: number;
+
+  /**
+   * End position of the sequence. If the coordinate system is 0-based then
+   * end 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.
+   */
+  readonly end?: number;
+
+  /**
+   * The score of an experimentally derived feature such as a p-value
+   * ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
+   */
+  readonly score?: Quantity;
+
+  /**
+   * Which method is used to get sequence quality.
+   */
+  readonly method?: CodeableConcept;
+
+  /**
+   * True positives, from the perspective of the truth data, i.e. the
+   * number of sites in the Truth Call Set for which there are paths
+   * through the Query Call Set that are consistent with all of the alleles
+   * at this site, and for which there is an accurate genotype call for the
+   * event.
+   */
+  readonly truthTP?: number;
+
+  /**
+   * True positives, from the perspective of the query data, i.e. the
+   * number of sites in the Query Call Set for which there are paths
+   * through the Truth Call Set that are consistent with all of the alleles
+   * at this site, and for which there is an accurate genotype call for the
+   * event.
+   */
+  readonly queryTP?: number;
+
+  /**
+   * False negatives, i.e. the number of sites in the Truth Call Set for
+   * which there is no path through the Query Call Set that is consistent
+   * with all of the alleles at this site, or sites for which there is an
+   * inaccurate genotype call for the event. Sites with correct variant but
+   * incorrect genotype are counted here.
+   */
+  readonly truthFN?: number;
+
+  /**
+   * False positives, i.e. the number of sites in the Query Call Set for
+   * which there is no path through the Truth Call Set that is consistent
+   * with this site. Sites with correct variant but incorrect genotype are
+   * counted here.
+   */
+  readonly queryFP?: number;
+
+  /**
+   * The number of false positives where the non-REF alleles in the Truth
+   * and Query Call Sets match (i.e. cases where the truth is 1/1 and the
+   * query is 0/1 or similar).
+   */
+  readonly gtFP?: number;
+
+  /**
+   * QUERY.TP / (QUERY.TP + QUERY.FP).
+   */
+  readonly precision?: number;
+
+  /**
+   * TRUTH.TP / (TRUTH.TP + TRUTH.FN).
+   */
+  readonly recall?: number;
+
+  /**
+   * Harmonic mean of Recall and Precision, computed as: 2 * precision *
+   * recall / (precision + recall).
+   */
+  readonly fScore?: number;
+
+  /**
+   * Receiver Operator Characteristic (ROC) Curve  to give
+   * sensitivity/specificity tradeoff.
+   */
+  readonly roc?: MolecularSequenceQualityRoc;
+}
+
+/**
+ * Receiver Operator Characteristic (ROC) Curve  to give
+ * sensitivity/specificity tradeoff.
+ */
+export interface MolecularSequenceQualityRoc {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Invidual data point representing the GQ (genotype quality) score
+   * threshold.
+   */
+  readonly score?: number[];
+
+  /**
+   * The number of true positives if the GQ score threshold was set to
+   * &quot;score&quot; field value.
+   */
+  readonly numTP?: number[];
+
+  /**
+   * The number of false positives if the GQ score threshold was set to
+   * &quot;score&quot; field value.
+   */
+  readonly numFP?: number[];
+
+  /**
+   * The number of false negatives if the GQ score threshold was set to
+   * &quot;score&quot; field value.
+   */
+  readonly numFN?: number[];
+
+  /**
+   * Calculated precision if the GQ score threshold was set to &quot;score&quot;
+   * field value.
+   */
+  readonly precision?: number[];
+
+  /**
+   * Calculated sensitivity if the GQ score threshold was set to &quot;score&quot;
+   * field value.
+   */
+  readonly sensitivity?: number[];
+
+  /**
+   * Calculated fScore if the GQ score threshold was set to &quot;score&quot; field
+   * value.
+   */
+  readonly fMeasure?: number[];
+}
+
+/**
+ * A sequence that is used as a reference to describe variants that are
+ * present in a sequence analyzed.
+ */
+export interface MolecularSequenceReferenceSeq {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Structural unit composed of a nucleic acid molecule which controls its
+   * own replication through the interaction of specific proteins at one or
+   * more origins of replication
+   * ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340)).
+   */
+  readonly chromosome?: CodeableConcept;
+
+  /**
+   * The Genome Build used for reference, following GRCh build versions
+   * e.g. 'GRCh 37'.  Version number must be included if a versioned
+   * release of a primary build was used.
+   */
+  readonly genomeBuild?: string;
+
+  /**
+   * A relative reference to a DNA strand based on gene orientation. The
+   * strand that contains the open reading frame of the gene is the &quot;sense&quot;
+   * strand, and the opposite complementary strand is the &quot;antisense&quot;
+   * strand.
+   */
+  readonly orientation?: string;
+
+  /**
+   * Reference identifier of reference sequence submitted to NCBI. It must
+   * match the type in the MolecularSequence.type field. For example, the
+   * prefix, &ldquo;NG_&rdquo; identifies reference sequence for genes, &ldquo;NM_&rdquo; for
+   * messenger RNA transcripts, and &ldquo;NP_&rdquo; for amino acid sequences.
+   */
+  readonly referenceSeqId?: CodeableConcept;
+
+  /**
+   * A pointer to another MolecularSequence entity as reference sequence.
+   */
+  readonly referenceSeqPointer?: Reference<MolecularSequence>;
+
+  /**
+   * A string like &quot;ACGT&quot;.
+   */
+  readonly referenceSeqString?: string;
+
+  /**
+   * An absolute reference to a strand. The Watson strand is the strand
+   * whose 5'-end is on the short arm of the chromosome, and the Crick
+   * strand as the one whose 5'-end is on the long arm.
+   */
+  readonly strand?: string;
+
+  /**
+   * Start position of the window on the reference sequence. If the
+   * coordinate system is either 0-based or 1-based, then start position is
+   * inclusive.
+   */
+  readonly windowStart?: number;
+
+  /**
+   * End position of the window on the reference sequence. If the
+   * coordinate system is 0-based then end 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.
+   */
+  readonly windowEnd?: number;
+}
+
+/**
+ * Configurations of the external repository. The repository shall store
+ * target's observedSeq or records related with target's observedSeq.
+ */
+export interface MolecularSequenceRepository {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Click and see / RESTful API / Need login to see / RESTful API with
+   * authentication / Other ways to see resource.
+   */
+  readonly type?: string;
+
+  /**
+   * URI of an external repository which contains further details about the
+   * genetics data.
+   */
+  readonly url?: string;
+
+  /**
+   * URI of an external repository which contains further details about the
+   * genetics data.
+   */
+  readonly name?: string;
+
+  /**
+   * Id of the variant in this external repository. The server will
+   * understand how to use this id to call for more info about datasets in
+   * external repository.
+   */
+  readonly datasetId?: string;
+
+  /**
+   * Id of the variantset in this external repository. The server will
+   * understand how to use this id to call for more info about variantsets
+   * in external repository.
+   */
+  readonly variantsetId?: string;
+
+  /**
+   * Id of the read in this external repository.
+   */
+  readonly readsetId?: string;
+}
+
+/**
+ * Information about chromosome structure variation.
+ */
+export interface MolecularSequenceStructureVariant {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Information about chromosome structure variation DNA change type.
+   */
+  readonly variantType?: CodeableConcept;
+
+  /**
+   * Used to indicate if the outer and inner start-end values have the same
+   * meaning.
+   */
+  readonly exact?: boolean;
+
+  /**
+   * Length of the variant chromosome.
+   */
+  readonly length?: number;
+
+  /**
+   * Structural variant outer.
+   */
+  readonly outer?: MolecularSequenceStructureVariantOuter;
+
+  /**
+   * Structural variant inner.
+   */
+  readonly inner?: MolecularSequenceStructureVariantInner;
+}
+
+/**
+ * Structural variant inner.
+ */
+export interface MolecularSequenceStructureVariantInner {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Structural variant inner start. If the coordinate system is either
+   * 0-based or 1-based, then start position is inclusive.
+   */
+  readonly start?: number;
+
+  /**
+   * Structural variant inner end. If the coordinate system is 0-based then
+   * end 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.
+   */
+  readonly end?: number;
+}
+
+/**
+ * Structural variant outer.
+ */
+export interface MolecularSequenceStructureVariantOuter {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * Structural variant outer start. If the coordinate system is either
+   * 0-based or 1-based, then start position is inclusive.
+   */
+  readonly start?: number;
+
+  /**
+   * Structural variant outer end. If the coordinate system is 0-based then
+   * end 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.
+   */
+  readonly end?: number;
+}
+
+/**
+ * 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.
+ */
+export interface MolecularSequenceVariant {
+
+  /**
+   * Unique id for the element within a resource (for internal references).
+   * This may be any string value that does not contain spaces.
+   */
+  readonly id?: string;
+
+  /**
+   * 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.
+   */
+  readonly extension?: Extension[];
+
+  /**
+   * May be used to represent additional information that is not part of
+   * the basic definition of the element and that modifies the
+   * understanding of the element in which it is contained and/or the
+   * understanding of the containing element's descendants. Usually
+   * modifier elements provide negation or qualification. 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.
+   * Applications processing a resource are required to check for modifier
+   * extensions.
+   *
+   * Modifier extensions SHALL NOT change the meaning of any elements on
+   * Resource or DomainResource (including cannot change the meaning of
+   * modifierExtension itself).
+   */
+  readonly modifierExtension?: Extension[];
+
+  /**
+   * 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.
+   */
+  readonly start?: number;
+
+  /**
+   * End position of the variant on the reference sequence. If the
+   * coordinate system is 0-based then end 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.
+   */
+  readonly end?: number;
+
+  /**
+   * 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.
+   */
+  readonly observedAllele?: string;
+
+  /**
+   * 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.
+   */
+  readonly referenceAllele?: string;
+
+  /**
+   * 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).
+   */
+  readonly cigar?: string;
+
+  /**
+   * A pointer to an Observation containing variant information.
+   */
+  readonly variantPointer?: Reference<Observation>;
+}