SpdiAllele sb-phenopackets

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.0.0)

Attributes

Type: object
Description: A single SPDI allele. The SPDI notation uses four fields and is written out as four elements delimited by colons S:P:D:I, where S = SequenceId P = Position , a 0-based coordinate for where the Deleted Sequence starts D = DeletedSequence , sequence for the deletion, can be empty I = InsertedSequence , sequence for the insertion, can be empty The SPDI notation represents variation as deletion of a sequence (D) at a given position (P) in reference sequence (S) followed by insertion of a replacement sequence (I) at that same position. Position 0 indicates a deletion that starts immediately before the first nucleotide, and position 1 represents a deletion interval that starts between the first and second residues, and so on. Either the deleted or the inserted interval can be empty, resulting a pure insertion or deletion. The deleted and inserted sequences in SPDI are all written on the positive strand for two-stranded molecules. See https://www.ncbi.nlm.nih.gov/variation/notation/

Properties

Property Type
deletedSequence string
id string
insertedSequence string
position integer
seqId string

deletedSequence

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deletedSequence Value Example
"T"

id

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id Value Example
"add example"

insertedSequence

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insertedSequence Value Example
"G"

position

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position Value Example
123256214

seqId

add description

seqId Value Example
"NC_000010.10"

SpdiAllele Value Example

{
   "deletedSequence" : "T",
   "id" : "id_abc_123",
   "insertedSequence" : "G",
   "position" : "123256214",
   "seqId" : "NC_000010.10"
}