U.S. flag

An official website of the United States government

NCBI Nestor notabilis Annotation Release 100

The RefSeq genome records for Nestor notabilis 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 Nestor notabilis Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Oct 29 2014
Date of submission of annotation to the public databases: Oct 31 2014
Software version: 6.1

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM69687v1GCF_000696875.1BGI06-05-2014Referenceunplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM69687v1
Genes and pseudogenes help14,954
  protein-coding14,753
  non-coding92
  pseudogenes109
  genes with variants743
mRNAs15,873
  fully-supported10,081
  with > 5% ab initio help2,009
  partial7,631
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)15,873
Other RNAs help173
  fully-supported59
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help59
CDSs15,886
  fully-supported10,081
  with > 5% ab initio help2,248
  partial7,640
  with major correction(s) help1,411
  known RefSeq (NP_) help0
  model RefSeq (XP_) help15,873

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
ASM69687v1GCF_000696875.15.60%17.67%

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