MolecularSequenceVariant

Raw data describing a biological sequence.

type MolecularSequenceVariant implements Element {
  start: Int
  end: Int
  observedAllele: String
  referenceAllele: String
  cigar: String
  variantPointer: Reference
  modifierExtension: [Extension]
  extension: [Extension]
  id: String
}

Fields

MolecularSequenceVariant.start ● Int scalar

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.

MolecularSequenceVariant.end ● Int scalar

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.

MolecularSequenceVariant.observedAllele ● String scalar

An allele is one of a set of coexisting sequence variants of a gene (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.

MolecularSequenceVariant.referenceAllele ● String scalar

An allele is one of a set of coexisting sequence variants of a gene (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.

MolecularSequenceVariant.cigar ● String scalar

Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation here.

MolecularSequenceVariant.variantPointer ● Reference object

A pointer to an Observation containing variant information.

MolecularSequenceVariant.modifierExtension ● [Extension] list object

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).

MolecularSequenceVariant.extension ● [Extension] list object

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.

MolecularSequenceVariant.id ● String scalar

Interfaces

Element interface

Base definition for all elements in a resource. If the element is present, it must have a value for at least one of the defined elements, an @id referenced from the Narrative, or extensions

Member Of

MolecularSequence object