NCBI Galeopterus variegatus Annotation Release 100

The RefSeq genome records for Galeopterus variegatus 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: Jul 18 2014
Date of submission of annotation to the public databases: Jul 23 2014
Software version: 6.0

Assemblies

Gene and feature statistics

Feature counts

Feature	G_variegatus-3.0.2
Genes and pseudogenes	30,024
protein-coding	23,081
non-coding	1,901
pseudogenes	5,042
genes with variants	5,046
mRNAs	32,091
fully-supported	24,919
with > 5% ab initio	3,192
partial	3,658
with filled gap(s)	0
known RefSeq (NM_)	0
model RefSeq (XM_)	32,091
Other RNAs	3,538
fully-supported	2,503
with > 5% ab initio	0
partial	0
with filled gap(s)	0
known RefSeq (NR_)	0
model RefSeq (XR_)	2,505
CDSs	32,351
fully-supported	24,919
with > 5% ab initio	3,712
partial	3,716
with major correction(s)	1,603
known RefSeq (NP_)	0
model RefSeq (XP_)	32,091

Detailed reports

Feature lengths

Feature	Count	Mean length (bp)	Median length (bp)	Min length (bp)	Max length (bp)
Genes	24,982	31,400	13,013	71	962,025
All transcripts	35,629	2,163	1,695	71	103,632
mRNA	32,091	2,311	1,826	72	103,632
misc_RNA	460	2,280	1,922	141	9,073
tRNA	1,033	74	74	71	86
lncRNA	2,045	867	611	93	6,637
Single-exon transcripts	2,017	1,120	945	72	9,095
coding transcripts (NM_/XM_ )	2,016	1,120	945	72	9,095
non-coding transcripts (NR_/XR_ )	1	461	461	461	461
CDSs	32,091	1,563	1,158	72	102,378
Exons	217,008	247	133	1	11,715
in coding transcripts (NM_/XM_ )	211,030	244	132	1	11,715
in non-coding transcripts (NR_/XR_ )	8,907	279	141	1	6,453
Introns	190,417	4,160	1,309	30	529,534
in coding transcripts (NM_/XM_ )	186,637	4,145	1,308	30	529,534
in non-coding transcripts (NR_/XR_ )	6,647	4,267	1,258	30	270,780

Transcripts per gene, exons per transcript

	Mean	Median	Min	Max
Number of transcripts per gene	1.4	1	1	25
Number of exons per transcript	9.39	7	1	314

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
Mus musculus GenBank	61,921	55,779 (90.08%)	55,779 (90.08%)	73.12%	76.30%
Mus musculus known RefSeq (NP_)	28,663	27,501 (95.95%)	27,501 (95.95%)	75.21%	76.17%
Homo sapiens GenBank	125,021	112,879 (90.29%)	112,879 (90.29%)	76.35%	78.92%
Homo sapiens known RefSeq (NP_)	37,925	36,700 (96.77%)	36,700 (96.77%)	77.25%	78.15%

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