NCBI Rattus norvegicus Annotation Release 104

The RefSeq genome records for Rattus norvegicus 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 Rattus norvegicus Annotation Release 104

Annotation release ID: 104
Date of Entrez queries for transcripts and proteins: Nov 22 2013
Date of submission of annotation to the public databases: Dec 9 2013
Software version: 5.2


The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Rnor_5.0GCF_000001895.4Rat Genome Sequencing Consortium03-16-2012Reference22 assembled chromosomes; unplaced scaffolds
Rn_CeleraGCF_000002265.2Celera Genomics12-06-2006Alternate21 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Genes and pseudogenes help37,72635,498
  with > 5% ab initio help611422
  known RefSeq (NM_) help17,33317,228
  model RefSeq (XM_)33,4419,722
  model RefSeq (XM_) with correction help367342
Other RNAs help13,97112,529
  with > 5% ab initio help00
  known RefSeq (NR_) help459449
  model RefSeq (XR_) help12,86311,421
  with > 5% ab initio help746515
  known RefSeq (NP_) help17,33117,225
  model RefSeq (XP_) help33,4419,722
  model RefSeq (XP_) with correction help367342

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

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

RefSeq transcript alignment quality report

The known RefSeq transcripts (NM_ and NR_ accessions) are a set of hiqh-quality transcripts maintained by the RefSeq group at NCBI. Alignment statistics for this group of transcripts, such as percent and number of sequences not aligning at all, percent best alignments split between multiple scaffolds, and percent alignments not covering the full CDS are indicative of the genome quality and are provided below.

Primary Assembly
Primary Assembly
Number of sequences retrieved from Entrez17,95317,953
Number (%) of sequences not aligning33 (0.18%)31 (0.17%)
Number (%) of sequences with multiple best alignments (split genes)255 (1.42%)96 (0.54%)
Number (%) of sequences with CDS coverage < 95% help961 (5.52%)700 (4.05%)

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

Assembly-assembly alignments of alternate to reference assembly

When multiple assemblies of good quality are available for the organism, the annotation of all is done in coordination. The alternate assemblies are aligned to the reference assembly and the best reciprocal best hits are used to identify corresponding regions, that can then be annotated together.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First PassTotal
Rn_Celera (Alternate) Coverage: 93.78%Rn_Celera (Alternate) Coverage: 94.41%
Rnor_5.0 (Reference) Coverage: 90.84%Rnor_5.0 (Reference) Coverage: 94.30%
Percent Identity: 99.93%Percent Identity: 99.81%


Write to the Help Desk