NCBI Oreochromis niloticus Annotation Release 102

The RefSeq genome records for Oreochromis niloticus 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
• 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

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 Oreochromis niloticus Annotation Release 102

Annotation release ID: 102
Date of Entrez queries for transcripts and proteins: Jul 28 2015
Date of submission of annotation to the public databases: Jul 30 2015
Software version: 6.4

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
Orenil1.1	GCF_000188235.2	Broad Institute	02-08-2012	Reference	23 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	Orenil1.1
Genes and pseudogenes	30,174
protein-coding	26,329
non-coding	3,508
pseudogenes	337
genes with variants	10,341
mRNAs	47,700
fully-supported	45,245
with > 5% ab initio	1,327
partial	3,050
with filled gap(s)	2,480
known RefSeq (NM_)	145
model RefSeq (XM_)	47,555
Other RNAs	5,694
fully-supported	5,071
with > 5% ab initio	0
partial	10
with filled gap(s)	10
known RefSeq (NR_)	0
model RefSeq (XR_)	5,071
CDSs	47,892
fully-supported	45,245
with > 5% ab initio	1,444
partial	2,467
with major correction(s)	817
known RefSeq (NP_)	145
model RefSeq (XP_)	47,555

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 26137 coding genes, 23381 genes had a protein with an alignment covering 50% or more of the query and 10797 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 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
Orenil1.1	GCF_000188235.2	3.13%	21.91%

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 Sequence 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

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