GC-AssemblyUnit
Defined in file genome_collection.asn
C++ class: CGC_AssemblyUnit
GC-AssemblyUnit ::= SEQUENCE
{
-- The identifier of this assembly
-- Contains: GenColl internal id, GenColl accession.version,
-- AGP id, UCSC name, Ensembl name
-- Types of DbTags used:
-- db "GenColl", tag id
-- db "GenColl", tag str
-- db "AGP", tag id
-- db "GenColl_Chain", tag id
-- "Ensembl_name" and "UCSC_name" will not appear in the Unit level since
-- these organizations do not define assembly-units.
id SET OF Dbtag,
-- 'class' defines the semantics of how to interpret this item
class INTEGER {
-- units for haploid/diploid assemblies
haploid-unit(1),
-- this unit represents one or more alternate loci for a haploid
-- assembly
alt-loci(2),
-- assembly-patch
assembly-patch(3),
-- stopper
other(255)
},
-- descriptors live in a shared data block
desc GC-AssemblyDesc,
-- collections of molecules for this assembly
mols SET OF GC-Replicon OPTIONAL,
-- On primary assembly-unit: here will be the unplaced sequences
-- On alt-loci: list of sequences aligned/unaligned to primary unit
other-sequences SET OF GC-TaggedSequences OPTIONAL,
-- statistics
-- "stats" field holds stats for all chromosomes combined:
-- ordered/unordered scaffolds
-- "unplaced-stats" holds stats for ChrUn which is omitted from "stats"
stats GC-SequenceStats OPTIONAL,
unplaced-stats SET OF GC-Scaf-stats OPTIONAL,
unplaced-unlocalized-stats SET OF GC-Scaf-stats OPTIONAL
}