NCBIMus musculus Annotation Release 105

TheRefSeqgenome records forMus musculus were annotated by theNCBI 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
• Alignment of the annotated proteins to a set of high-quality proteins: The number of annotated proteins with hits to a set of high-quality proteins
• 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 theNCBI Eukaryotic Genome Annotation Pipeline page.

Annotation Release information

This annotation should be referred to as NCBIMus musculus Annotation Release 105

Annotation release ID: 105
Date of Entrez queries for transcripts and proteins: Jan 16 2015
Date of submission of annotation to the public databases: Feb 9 2015
Software version:6.2

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
GRCm38.p3	GCF_000001635.23	Genome Reference Consortium	03-20-2014	Reference	22 assembled chromosomes; unplaced scaffolds
Mm_Celera	GCF_000002165.2	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	GRCm38.p3	GRCm38.p3 C57BL/6J	GRCm38.p3 All Alt Loci	GRCm38.p3 PATCHES	Mm_Celera
Genes and pseudogenes	46,432	46,254	1,692	194	43,586
protein-coding	22,549	22,484	1,064	91	21,340
non-coding	14,508	14,451	354	78	13,834
pseudogenes	9,375	9,319	274	25	8,412
genes with variants	18,073	18,033	587	66	8,930
placed on multiple assembly-units	1,678	na	343	na	na
mRNAs	76,131	74,221	3,007	226	29,973
fully-supported	75,628	73,755	2,973	223	29,638
with > 5% ab initio	272	257	14	1	181
partial	151	146	100	7	4,149
with filled gap(s)	2	2	0	0	12
placed on multiple assembly-units	1,289	na	305	na	na
known RefSeq (NM_)	28,881	28,871	1,219	114	28,130
model RefSeq (XM_)	47,250	45,350	1,788	112	1,843
Other RNAs	31,500	30,572	875	172	25,221
fully-supported	30,018	29,281	788	142	24,035
with > 5% ab initio	0	0	0	0	0
partial	9	11	4	2	307
with filled gap(s)	0	0	0	0	12
placed on multiple assembly-units	117	na	25	na	na
known RefSeq (NR_)	4,276	4,276	135	58	4,120
model RefSeq (XR_)	25,771	25,033	654	84	19,939
CDSs	76,759	74,712	3,139	226	30,259
fully-supported	75,628	73,755	2,973	223	29,638
with > 5% ab initio	329	313	15	1	216
partial	142	132	87	6	2,854
with major correction(s)	239	168	70	8	2,761
known RefSeq (NP_)	28,881	28,871	1,214	114	28,104
model RefSeq (XP_)	47,250	45,350	1,788	112	1,843

Detailed reports

Alignment of the annotated proteins to a set of high-quality proteins

The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 21993 coding genes in the reference assembly GRCm38.p3, 21222 genes had a protein with an alignment covering 50% or more of the query and 19365 had an alignment covering 95% or more of the query. Out of 21013 coding genes in the alternate assembly Mm_Celera, 20442 genes had a protein with an alignment covering 50% or more of the query and 18865 had an alignment covering 95% or more of the query.

Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.

Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.

Query: annotated proteins
Target: UniProtKB/Swiss-Prot curated proteins

Masking of genomic sequence

Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked byWindowMasker andRepeatMasker 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 RepeatMasker only.

Assembly name	Assembly accession	% Masked with RepeatMasker	% Masked with WindowMasker
GRCm38.p3	GCF_000001635.23	44.02%	35.38%
Mm_Celera	GCF_000002165.2	38.56%	28.80%

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 bySplign orProSplign and passed toGnomon, 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 theTranscript alignments section or aligned with short reads and reported in theShort read transcript alignments section.

Transcript alignments

RefSeq transcript alignment quality report

The knownRefSeq transcripts (NM_ and NR_ accessions) are a set of hiqh-quality transcripts maintained by theRefSeq 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.

	GRCm38.p3 Primary Assembly	Mm_Celera Primary Assembly
Number of sequences retrieved from Entrez	33,603	33,603
Number (%) of sequences not aligning	14 (0.04%)	395 (1.18%)
Number (%) of sequences with multiple best alignments (split genes)	27 (0.08%)	328 (1.00%)
Number (%) of sequences with CDS coverage < 95%	52 (0.18%)	1,903 (6.70%)

Short read transcript alignments

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

  Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)  Show alignments statistics, by run (ERR, SRR, DRR)

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 theNCBI Genome Remapping Service page.

First Pass	Total
GRCm38.p3 (Current) Coverage: 99.96%	GRCm38.p3 (Current) Coverage: 99.99%
GRCm38.p2 (Previous) Coverage: 100.00%	GRCm38.p2 (Previous) Coverage: 100.00%
Percent Identity: 100.00%	Percent Identity: 99.99%

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 theNCBI Genome Remapping Service page.

First Pass	Total
Mm_Celera (Alternate) Coverage: 96.43%	Mm_Celera (Alternate) Coverage: 97.17%
GRCm38.p3 (Reference) Coverage: 87.35%	GRCm38.p3 (Reference) Coverage: 90.83%
Percent Identity: 99.58%	Percent Identity: 99.48%

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