Copy Number Count

A copy number count is used to represent the integer number of copies of a Sequence Location in a genome.

Definition and Information Model

Note

This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

The absolute count of discrete copies of a Location within a system (e.g. genome, cell, etc.).

GA4GH Digest

Prefix	Inherent
CN	[‘copies’, ‘location’, ‘type’]

Information Model

Some CopyNumberCount attributes are inherited from Variation.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
digest		string	0..1	A sha512t24u digest created using the VRS Computed Identifier algorithm.
expressions	⋮	Expression	0..m
type		string	1..1	MUST be “CopyNumberCount”
location		iriReference | Location	1..1	The location of the subject of the copy count.
copies		integer | Range	1..1	The integral number of copies of the subject in a system

Example

{
  "id": "ga4gh:CN.ezEUXykQvIhX8jHADILwC9f8k-jp8tZC",
  "type": "CopyNumberCount",
  "copies": [3, null],
  "location": {
    "sequenceReference": {
      "refgetAccession": "SQ.jdEWLvLvT8827O59m1Agh5H3n6kTzBsJ",
      "type": "SequenceReference"
    },
    "end": 44909393,
    "start": 44905795,
    "type": "SequenceLocation"
  }
}