NCBI Tupaia chinensis Annotation Release 100

The RefSeq genome records for Tupaia chinensis 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 Tupaia chinensis Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Nov 19 2013
Date of submission of annotation to the public databases: Dec 3 2013
Software version: 5.2

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
TupChi_1.0GCF_000334495.1BGI01-31-2013Referenceunplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureTupChi_1.0
Genes and pseudogenes help35,818
  protein-coding20,650
  non-coding2,877
  pseudogenes12,291
mRNAs32,722
  fully-supported27,575
  with > 5% ab initio help2,835
  partial1,276
  known RefSeq (NM_) help0
  model RefSeq (XM_)32,722
  model RefSeq (XM_) with correction help1,447
Other RNAs help4,918
  fully-supported4,524
  with > 5% ab initio help0
  partial0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help4,525
CDSs32,848
  fully-supported27,575
  with > 5% ab initio help3,299
  partial1,283
  known RefSeq (NP_) help0
  model RefSeq (XP_) help32,722
  model RefSeq (XP_) with correction help1,447

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
TupChi_1.0GCF_000334495.120.74%37.58%

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

The following short reads (RNA-Seq) from the Short Read Archive were also used for gene prediction:

  Hide alignments statistics

Protein alignments

References

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