NCBI Rattus norvegicus Annotation Release 105

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:

• Annotation Release information: The name of the release, important dates, the software version
• Assemblies: A brief description of the annotated assembly(ies)
• Gene and feature statistics: The counts and characteristics of the annotated features
• Masking of genomic sequence: How much of the genome was masked
• Transcript and protein alignments: The number and type of evidence retrieved from public databases and used for gene prediction
• Similarity of current and previous assembly: The similarity of the current and previous assembly
• Similarity of alternate and reference assemblies: The similarity of the alternate assemblies to the reference

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 105

Annotation release ID: 105
Date of Entrez queries for transcripts and proteins: Jul 18 2014
Date of submission of annotation to the public databases: Aug 7 2014
Software version: 6.0

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
Rnor_6.0	GCF_000001895.5	Rat Genome Sequencing Consortium	07-01-2014	Reference	23 assembled chromosomes; unplaced scaffolds
Rn_Celera	GCF_000002265.2	Celera Genomics	12-06-2006	Alternate	21 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	Rnor_6.0	Rn_Celera
Genes and pseudogenes	37,224	34,490
protein-coding	23,460	21,927
non-coding	6,538	5,935
pseudogenes	7,226	6,628
genes with variants	11,686	3,260
mRNAs	50,651	26,651
fully-supported	49,039	25,553
with > 5% ab initio	798	498
partial	1,449	1,932
with filled gap(s)	86	80
known RefSeq (NM_)	17,349	17,286
model RefSeq (XM_)	33,302	9,365
Other RNAs	10,855	9,290
fully-supported	10,138	8,599
with > 5% ab initio	0	0
partial	5	9
with filled gap(s)	5	4
known RefSeq (NR_)	532	519
model RefSeq (XR_)	9,635	8,101
CDSs	51,127	27,048
fully-supported	49,039	25,553
with > 5% ab initio	914	592
partial	1,086	1,486
with major correction(s)	2,146	1,769
known RefSeq (NP_)	17,347	17,283
model RefSeq (XP_)	33,302	9,365

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 name	Assembly accession	% Masked with RepeatMasker	% Masked with WindowMasker
Rnor_6.0	GCF_000001895.5	41.93%	32.29%
Rn_Celera	GCF_000002265.2	41.49%	31.75%

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.

	Rnor_6.0 Primary Assembly	Rn_Celera Primary Assembly
Number of sequences retrieved from Entrez	18,059	18,059
Number (%) of sequences not aligning	36 (0.20%)	31 (0.17%)
Number (%) of sequences with multiple best alignments (split genes)	70 (0.39%)	105 (0.59%)
Number (%) of sequences with CDS coverage < 95%	460 (2.64%)	703 (4.05%)

Short read transcript alignments

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

  Hide alignments statistics

Protein alignments

Assembly-assembly alignments of current to previous assembly

When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.

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 Pass	Total
Rnor_6.0 (Current) Coverage: 93.53%	Rnor_6.0 (Current) Coverage: 94.62%
Rnor_5.0 (Previous) Coverage: 99.23%	Rnor_5.0 (Previous) Coverage: 99.54%
Percent Identity: 99.99%	Percent Identity: 99.98%

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 Pass	Total
Rn_Celera (Alternate) Coverage: 95.79%	Rn_Celera (Alternate) Coverage: 96.81%
Rnor_6.0 (Reference) Coverage: 87.49%	Rnor_6.0 (Reference) Coverage: 89.89%
Percent Identity: 99.90%	Percent Identity: 99.77%

References

• RefSeq: Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Nucleic Acids Research 2014, 42(Database issue):D756-63
• RepeatMasker: Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. http://www.repeatmasker.org
• WindowMasker: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Bioinformatics 2006, 2:134-41
• Splign: Kapustin Y, Souvorov A, Tatusova T, Lipman D. Biology Direct 2008, 3:20