NCBI Struthio camelus australis Annotation Release 100

The RefSeq genome records for Struthio camelus australis 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: Oct 14 2014
Date of submission of annotation to the public databases: Oct 15 2014
Software version: 6.1

Assemblies

Gene and feature statistics

Feature counts

Feature	ASM69896v1
Genes and pseudogenes	16,512
protein-coding	14,592
non-coding	1,821
pseudogenes	99
genes with variants	4,596
mRNAs	25,425
fully-supported	20,702
with > 5% ab initio	1,749
partial	1,347
with filled gap(s)	0
known RefSeq (NM_)	0
model RefSeq (XM_)	25,425
Other RNAs	3,747
fully-supported	3,583
with > 5% ab initio	0
partial	0
with filled gap(s)	0
known RefSeq (NR_)	0
model RefSeq (XR_)	3,583
CDSs	25,440
fully-supported	20,702
with > 5% ab initio	2,477
partial	1,349
with major correction(s)	921
known RefSeq (NP_)	0
model RefSeq (XP_)	25,425

Detailed reports

Feature lengths

Feature	Count	Mean length (bp)	Median length (bp)	Min length (bp)	Max length (bp)
Genes	16,413	36,403	15,987	71	1,258,879
All transcripts	29,172	3,514	2,925	71	104,621
mRNA	25,425	3,627	3,029	111	104,621
misc_RNA	754	3,945	3,371	437	16,483
tRNA	164	74	73	71	84
lncRNA	2,829	2,580	1,648	109	15,652
Single-exon transcripts	553	1,691	1,092	149	11,419
coding transcripts (NM_/XM_ )	553	1,691	1,092	149	11,419
CDSs	25,425	1,945	1,455	96	103,638
Exons	183,806	311	131	1	17,106
in coding transcripts (NM_/XM_ )	174,662	296	130	1	17,106
in non-coding transcripts (NR_/XR_ )	14,047	457	139	2	15,470
Introns	166,466	3,931	1,130	30	822,126
in coding transcripts (NM_/XM_ )	159,661	3,807	1,112	30	822,126
in non-coding transcripts (NR_/XR_ )	11,591	5,403	1,460	30	276,103

Transcripts per gene, exons per transcript

	Mean	Median	Min	Max
Number of transcripts per gene	1.77	1	1	46
Number of exons per transcript	12.09	9	1	316

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
Xenopus GenBank	32,100	28,338 (88.28%)	28,338 (88.28%)	70.17%	71.94%
Xenopus known RefSeq (NP_)	19,906	17,718 (89.01%)	17,718 (89.01%)	70.16%	72.20%
Xenopus (Silurana) tropicalis high-quality model RefSeq (XP_)	5,421	4,816 (88.84%)	4,816 (88.84%)	68.10%	67.36%
Aves high-quality model RefSeq (XP_)	26,126	25,580 (97.91%)	25,580 (97.91%)	78.44%	82.05%
Aves GenBank	11,836	10,203 (86.20%)	10,203 (86.20%)	74.93%	76.39%
Aves known RefSeq (NP_)	7,200	6,845 (95.07%)	6,845 (95.07%)	77.63%	77.35%
Homo sapiens known RefSeq (NP_)	38,121	31,796 (83.41%)	31,796 (83.41%)	68.91%	66.70%

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