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Note: 
The NCBI eukaryotic genome annotation pipeline is now using 
Annotation Release numbers.

To avoid confusion between the independent notions of a genome 
assembly and its annotation, NCBI is now using Annotation Release 
numbers to designate annotation versions. 
Annotation Release numbers:
- are integer values that increment each time the genome annotation is 
updated.
- have initial values starting at 100 or higher.
- are incremented independently for each organism. This means that 
different organisms may have the same release number (eg. Homo sapiens 
Annotation Release 103, Mus musculus Annotation Release 103) but the 
two annotation runs are not connected. In addition, differences in 
the release number value for different organisms does not imply 
anything about how up-to-date the annotation is for that organism 
(e.g., Mus musculus Annotation Release 102 could be a newer dataset 
than Homo sapiens Annotation Release 103).
- are used for the set of annotations calculated on one or more genome 
assemblies. For instance, Homo sapiens Annotation Release 103 includes 
an updated annotation for the reference assembly, the HuRef assembly, 
and the CRA_TCAGchr7v2 chromosome 7 assembly.

Therefore, a specific genome annotation dataset is specified by the 
combination of two identifiers, the NCBI taxonomy ID or species name 
and the Annotation Release number. The specific Annotation Release 
has pointers to the assembly accession.versions that were the 
substrates for the annotation run.


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Release name: NCBI Homo sapiens Annotation Release 104
Release date: 2 November 2012

Freeze date for component genomic sequences: 16 October 2012
Freeze date for other genomic sequences: 20 October 2012
Freeze date for mRNAs/ESTs used for annotation: 20 October 2012

Assemblies in NCBI Homo sapiens Annotation Release 104:

* GRCh37.p10 (GCF_000001405.22)
The human genome assembly released August 31, 2012 by the Genome 
Reference Consortium. The full GRCh37.p10 assembly is comprised of the
following 12 assembly-units:

#Assembly-unit id	Assembly-unit name
GCF_000001305.13	Primary_Assembly
GCF_000001315.1	ALT_REF_LOCI_1
GCF_000001325.2	ALT_REF_LOCI_2
GCF_000001335.1	ALT_REF_LOCI_3
GCF_000001345.1	ALT_REF_LOCI_4
GCF_000001355.1	ALT_REF_LOCI_5
GCF_000001365.2	ALT_REF_LOCI_6
GCF_000001375.1	ALT_REF_LOCI_7
GCF_000001385.1	ALT_REF_LOCI_8
GCF_000001395.1	ALT_REF_LOCI_9
GCF_000005045.9	PATCHES
GCF_000006015.1	 non-nuclear

The primary assembly represents the assembled chromosomes, plus any 
unlocalized or unplaced sequence that represent the non-redundant, 
haploid assembly. The nine alternate loci represent regions for which
there is large scale variation from the sequence in the primary 
assembly. The PATCHES assembly-unit contain new alternate loci (novel 
patch) or regions where the sequence was improved (fix patch). 
PATCHES are minor updates to the assembly and will be incorporated 
into the primary assembly or appropritate alternative loci in the 
next version of the assembly.

For more details, see: 
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml.

The non-nuclear assembly-unit contains the NCBI Reference Sequence 
(RefSeq) for the human mitochondrion genome.

The primary assembly and alternative loci are identical in GRCh37 and 
GRCh37.p10.

GRCh37.p10 is the reference assembly.


* HuRef (GCF_000002125.1)
The J Craig Venter Institute whole-genome shotgun assembly 
(ABBA00000000.1, May 2007). See: 
http://www.jcvi.org/research/huref/). 
This assembly represents a composite haploid version of the diploid 
genome sequence from a single individual (J. Craig Venter).


* CRA_TCAGchr7v2 (GCF_000002135.2)
The Center for Applied Genomics at the Hospital for Sick Children 
(Toronto) chromosome 7 assembly, (April 2004).


* CHM1_1.0 (GCF_000306695.1)
The Washington University School of Medicine and National Center for 
Biotechnology Information whole-genome shotgun assembly 
(AMYH00000000.1, October 2012).


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