NCBI Orycteropus afer afer Annotation Release 100

The RefSeq genome records for Orycteropus afer afer were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

The annotation products are available in the sequence databases and on the FTP site.

This report provides:

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.


Annotation Release information

This annotation should be referred to as NCBI Orycteropus afer afer Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: May 9 2014
Date of submission of annotation to the public databases: May 14 2014
Software version: 6.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
OryAfe1.0GCF_000298275.1Broad Institute09-20-2012Reference1 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

Counts and length of annotated features are provided below for each assembly.

Feature counts

FeatureOryAfe1.0
Genes and pseudogenes help22,573
  protein-coding19,607
  non-coding54
  pseudogenes2,912
  genes with variants3,372
mRNAs25,531
  fully-supported18,329
  with > 5% ab initio help3,093
  partial537
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)25,531
Other RNAs help618
  fully-supported13
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help13
CDSs25,640
  fully-supported18,329
  with > 5% ab initio help3,291
  partial561
  with major correction(s) help1,150
  known RefSeq (NP_) help0
  model RefSeq (XP_) help25,531

Detailed reports

Masking of genomic sequence

Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker for each assembly. RepeatMasker results are only used for organisms for which a comprehensive repeat library is available.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
OryAfe1.0GCF_000298275.124.41%38.66%

Transcript and protein alignments

The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign or ProSplign and passed to Gnomon, NCBI's gene prediction software.

Depending on the other evidence available, long 454 reads (with average length above 250 nt) may be aligned as traditional evidence and reported in the Transcript alignments section or aligned with short reads and reported in the Short read transcript alignments section.

Transcript alignments

Short read transcript alignments

No short read transcripts were used in this annotation

Protein alignments

References

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