NCBI Stegastes partitus Annotation Release 100

The RefSeq genome records for Stegastes partitus 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

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.

Annotation Release information

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jun 16 2014
Date of submission of annotation to the public databases: Jun 19 2014
Software version: 6.0

Assemblies

Gene and feature statistics

Feature counts

Feature	Stegastes_partitus-1.0.2
Genes and pseudogenes	23,869
protein-coding	22,655
non-coding	1,023
pseudogenes	191
genes with variants	5,204
mRNAs	31,597
fully-supported	27,959
with > 5% ab initio	1,380
partial	1,174
with filled gap(s)	1
known RefSeq (NM_)	0
model RefSeq (XM_)	31,597
Other RNAs	2,398
fully-supported	1,354
with > 5% ab initio	0
partial	0
with filled gap(s)	0
known RefSeq (NR_)	0
model RefSeq (XR_)	1,354
CDSs	31,672
fully-supported	27,959
with > 5% ab initio	1,603
partial	1,186
with major correction(s)	350
known RefSeq (NP_)	0
model RefSeq (XP_)	31,597

Detailed reports

Feature lengths

Feature	Count	Mean length (bp)	Median length (bp)	Min length (bp)	Max length (bp)
Genes	23,678	18,904	9,521	70	711,380
All transcripts	33,995	3,012	2,354	64	103,810
mRNA	31,597	3,185	2,494	165	103,810
misc_RNA	301	2,696	2,261	94	14,967
tRNA	1,044	74	73	64	86
lncRNA	1,053	830	564	83	7,465
Single-exon transcripts	771	1,590	1,353	211	6,846
coding transcripts (NM_/XM_ )	771	1,590	1,353	211	6,846
CDSs	31,597	2,020	1,419	99	102,558
Exons	256,113	263	133	1	17,313
in coding transcripts (NM_/XM_ )	252,736	262	133	1	17,313
in non-coding transcripts (NR_/XR_ )	5,600	278	126	1	7,275
Introns	231,832	1,775	490	30	708,737
in coding transcripts (NM_/XM_ )	229,691	1,759	488	30	708,737
in non-coding transcripts (NR_/XR_ )	4,319	2,473	559	30	694,145

Transcripts per gene, exons per transcript

	Mean	Median	Min	Max
Number of transcripts per gene	1.4	1	1	26
Number of exons per transcript	12.03	9	1	255

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.

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:

Protein alignments

Source	Number of sequences retrieved from Entrez	Number (%) of sequences aligned by ProSplign	Number (%) of sequences passed to Gnomon	Average % identity	Average % coverage
Actinopterygii high-quality model RefSeq (XP_)	118,644	117,271 (98.84%)	117,271 (98.84%)	71.69%	77.31%
Actinopterygii GenBank	70,131	65,473 (93.36%)	65,473 (93.36%)	69.79%	76.41%
Actinopterygii known RefSeq (NP_)	22,176	21,268 (95.91%)	21,268 (95.91%)	69.06%	75.11%
Homo sapiens known RefSeq (NP_)	37,413	31,288 (83.63%)	31,288 (83.63%)	65.97%	63.98%

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