NCBI Saccoglossus kowalevskii Annotation Release 101

The RefSeq genome records for Saccoglossus kowalevskii 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: 101
Date of Entrez queries for transcripts and proteins: Feb 4 2014
Date of submission of annotation to the public databases: Feb 19 2014
Software version: 5.2

Assemblies

Gene and feature statistics

Feature counts

Feature	Skow_1.1
Genes and pseudogenes	21,837
protein-coding	20,922
non-coding	678
pseudogenes	237
genes with variants	751
mRNAs	22,098
fully-supported	9,097
with > 5% ab initio	11,136
partial	3,004
known RefSeq (NM_)	468
model RefSeq (XM_)	21,630
model RefSeq (XM_) with correction	210
Other RNAs	10,646
fully-supported	674
with > 5% ab initio	0
partial	1
known RefSeq (NR_)	85
model RefSeq (XR_)	591
CDSs	22,098
fully-supported	9,097
with > 5% ab initio	11,518
partial	2,982
known RefSeq (NP_)	468
model RefSeq (XP_)	21,630
model RefSeq (XP_) with correction	210

Detailed reports

Feature lengths

Feature	Count	Mean length (bp)	Median length (bp)	Min length (bp)	Max length (bp)
Genes	21,600	13,122	7,418	69	210,238
All transcripts	32,744	1,283	924	20	56,859
mRNA	22,098	1,845	1,398	172	56,859
misc_RNA	50	2,322	2,038	321	6,907
miRNA	108	22	22	20	24
tRNA	9,946	75	73	67	88
lncRNA	541	698	539	77	9,343
rRNA	1	169	169	169	169
Single-exon transcripts	2,630	1,104	963	243	12,258
coding transcripts (NM_/XM_ )	2,630	1,104	963	243	12,258
CDSs	22,098	1,486	1,104	171	56,859
Exons	164,851	234	143	1	12,258
in coding transcripts (NM_/XM_ )	163,091	234	143	1	12,258
in non-coding transcripts (NR_/XR_ )	2,044	231	126	2	8,820
Introns	143,016	1,737	673	21	114,895
in coding transcripts (NM_/XM_ )	141,827	1,736	673	21	114,895
in non-coding transcripts (NR_/XR_ )	1,464	1,865	654	31	51,885

Transcripts per gene, exons per transcript

	Mean	Median	Min	Max
Number of transcripts per gene	1.06	1	1	67
Number of exons per transcript	7.74	6	1	149

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

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.

	Skow_1.1 Primary Assembly
Number of sequences retrieved from Entrez	555
Number (%) of sequences not aligning	0 (0.00%)
Number (%) of sequences with multiple best alignments (split genes)	29 (5.23%)
Number (%) of sequences with CDS coverage < 95%	50 (10.66%)

Short read transcript alignments

The following short reads (RNA-Seq) from the Short 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
Hemichordata GenBank	105	104 (99.05%)	104 (99.05%)	80.24%	79.79%
Same-species GenBank	214	212 (99.07%)	212 (99.07%)	88.85%	85.10%
Same-species known RefSeq (NP_)	469	467 (99.57%)	467 (99.57%)	89.38%	88.15%
Drosophila melanogaster known RefSeq (NP_)	27,764	11,807 (42.53%)	11,807 (42.53%)	62.56%	48.84%
Ciona intestinalis known RefSeq (NP_)	947	574 (60.61%)	574 (60.61%)	59.19%	38.00%
Homo sapiens known RefSeq (NP_)	36,861	22,449 (60.90%)	22,449 (60.90%)	59.87%	42.86%

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