NCBI Tinamus guttatus Annotation Release 100

The RefSeq genome records for Tinamus guttatus 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

This annotation should be referred to as NCBI Tinamus guttatus Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Nov 6 2014
Date of submission of annotation to the public databases: Nov 13 2014
Software version: 6.1

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
ASM70537v2	GCF_000705375.1	BGI	08-05-2014	Reference	unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	ASM70537v2
Genes and pseudogenes	16,984
protein-coding	15,742
non-coding	1,051
pseudogenes	191
genes with variants	1,260
mRNAs	17,873
fully-supported	9,815
with > 5% ab initio	4,250
partial	3,994
with filled gap(s)	0
known RefSeq (NM_)	0
model RefSeq (XM_)	17,873
Other RNAs	1,362
fully-supported	1,116
with > 5% ab initio	0
partial	0
with filled gap(s)	0
known RefSeq (NR_)	0
model RefSeq (XR_)	1,117
CDSs	17,892
fully-supported	9,815
with > 5% ab initio	4,656
partial	4,002
with major correction(s)	1,192
known RefSeq (NP_)	0
model RefSeq (XP_)	17,873

Detailed reports

Feature lengths

Feature	Count	Mean length (bp)	Median length (bp)	Min length (bp)	Max length (bp)
Genes	16,793	21,278	10,451	64	661,347
All transcripts	19,235	1,738	1,329	64	101,087
mRNA	17,873	1,845	1,409	64	101,087
misc_RNA	80	1,840	1,636	133	5,550
tRNA	245	74	72	68	84
lncRNA	1,037	289	219	80	3,034
Single-exon transcripts	867	1,004	905	64	7,905
coding transcripts (NM_/XM_ )	867	1,004	905	64	7,905
CDSs	17,873	1,618	1,209	64	100,102
Exons	159,916	177	126	1	17,106
in coding transcripts (NM_/XM_ )	156,729	178	127	1	17,106
in non-coding transcripts (NR_/XR_ )	3,794	109	80	2	3,292
Introns	143,135	2,394	857	30	331,996
in coding transcripts (NM_/XM_ )	141,004	2,361	853	30	331,996
in non-coding transcripts (NR_/XR_ )	2,714	4,224	1,255	30	231,565

Transcripts per gene, exons per transcript

	Mean	Median	Min	Max
Number of transcripts per gene	1.14	1	1	27
Number of exons per transcript	9.94	7	1	296

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
ASM70537v2	GCF_000705375.1	3.54%	18.49%

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

Source	Number of sequences retrieved from Entrez	Number (%) of sequences aligned by Splign	Number (%) of sequences passed to Gnomon	Average % identity	Average % coverage
Aves known RefSeq (NM_/NR_)	1,357	961 (70.82%)	515 (37.95%)	91.65%	81.93%
Aves Genbank	8,778	4,999 (56.95%)	2,302 (26.22%)	90.31%	81.78%
Aves TSA	104,203	33,961 (32.59%)	765 (0.73%)	96.37%	89.66%
Aves EST	156,310	35,157 (22.49%)	20,309 (12.99%)	90.76%	95.96%
Gallus gallus known RefSeq (NM_/NR_)	6,844	5,359 (78.30%)	1,978 (28.90%)	90.21%	77.04%
Gallus gallus Genbank	29,352	16,289 (55.50%)	6,469 (22.04%)	89.95%	79.33%
Gallus gallus TSA	28	15 (53.57%)	1 (3.57%)	97.00%	92.00%
Gallus gallus EST	600,027	126,120 (21.02%)	71,764 (11.96%)	90.52%	96.26%

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)

Sample Id	Track name	Number of reads	Number (%) of aligned reads	Number (%) spliced reads	Number of introns
All	Aggregate of all aligned samples	587,599,446	202,954,484 (34.54%)	67,698,123 (11.52%)	154,313
SAMN00857833	Struthio camelus, brain, male (pool 1, SAMN00857833)	53,237,500	19,275,923 (36.21%)	6,047,394 (11.36%)	128,809
SAMN00858080	Struthio camelus, brain, male (pool 2, SAMN00858080)	45,014,800	16,045,846 (35.65%)	4,943,298 (10.98%)	125,572
SAMN00990651	Struthio camelus, brain, male (pool 3, SAMN00990651)	32,639,550	11,665,554 (35.74%)	3,555,632 (10.89%)	120,700
SAMN00990826	Struthio camelus, brain, female (pool 1, SAMN00990826)	55,611,376	19,785,738 (35.58%)	6,100,990 (10.97%)	128,653
SAMN00990827	Struthio camelus, brain, female (pool 2, SAMN00990827)	45,318,840	16,322,649 (36.02%)	5,052,639 (11.15%)	125,903
SAMN00992209	Struthio camelus, brain, female (pool 3, SAMN00992209)	41,562,376	14,779,079 (35.56%)	4,660,209 (11.21%)	124,531
SAMN01041319	Struthio camelus, liver, male (pool 1, SAMN01041319)	68,403,442	22,862,269 (33.42%)	8,063,768 (11.79%)	120,563
SAMN01041452	Struthio camelus, liver, male (pool 2, SAMN01041452)	69,179,952	23,496,816 (33.96%)	8,423,634 (12.18%)	119,329
SAMN01048167	Struthio camelus, liver, male (pool 3, SAMN01048167)	48,949,606	16,834,187 (34.39%)	5,987,094 (12.23%)	116,369
SAMN01048183	Struthio camelus, liver, female (pool 1, SAMN01048183)	32,726,248	10,887,164 (33.27%)	3,811,179 (11.65%)	110,471
SAMN01055118	Struthio camelus, liver, female (pool 2, SAMN01055118)	70,060,076	22,713,827 (32.42%)	8,111,823 (11.58%)	116,151
SAMN01055119	Struthio camelus, liver, female (pool 3, SAMN01055119)	24,895,680	8,285,432 (33.28%)	2,940,463 (11.81%)	101,480

Show alignments statistics, by run (ERR, SRR, DRR)

Run	Experiment	Project	Sample	Number of reads	Number (%) of aligned reads	Number (%) spliced reads
SRR488565	SRX142690	SRP012236	SAMN00857833	53,237,500	19,275,923 (36.21%)	6,047,394 (11.36%)
SRR488687	SRX143226	SRP012236	SAMN00858080	45,014,800	16,045,846 (35.65%)	4,943,298 (10.98%)
SRR493274	SRX145593	SRP012236	SAMN00990651	32,639,550	11,665,554 (35.74%)	3,555,632 (10.89%)
SRR493935	SRX145873	SRP012236	SAMN00990826	55,611,376	19,785,738 (35.58%)	6,100,990 (10.97%)
SRR496182	SRX145874	SRP012236	SAMN00990827	45,318,840	16,322,649 (36.02%)	5,052,639 (11.15%)
SRR496214	SRX147559	SRP012236	SAMN00992209	41,562,376	14,779,079 (35.56%)	4,660,209 (11.21%)
SRR504696	SRX151868	SRP012236	SAMN01041319	68,403,442	22,862,269 (33.42%)	8,063,768 (11.79%)
SRR507781	SRX153141	SRP012236	SAMN01041452	69,179,952	23,496,816 (33.96%)	8,423,634 (12.18%)
SRR513096	SRX154477	SRP012236	SAMN01048167	48,949,606	16,834,187 (34.39%)	5,987,094 (12.23%)
SRR513126	SRX154500	SRP012236	SAMN01048183	32,726,248	10,887,164 (33.27%)	3,811,179 (11.65%)
SRR513754	SRX154849	SRP012236	SAMN01055118	70,060,076	22,713,827 (32.42%)	8,111,823 (11.58%)
SRR513755	SRX154850	SRP012236	SAMN01055119	24,895,680	8,285,432 (33.28%)	2,940,463 (11.81%)

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	32,103	28,068 (87.43%)	28,068 (87.43%)	70.37%	69.62%
Xenopus known RefSeq (NP_)	19,906	17,559 (88.21%)	17,559 (88.21%)	70.47%	69.75%
Xenopus (Silurana) tropicalis high-quality model RefSeq (XP_)	5,421	4,735 (87.35%)	4,735 (87.35%)	68.42%	64.54%
Aves high-quality model RefSeq (XP_)	26,126	25,487 (97.55%)	25,487 (97.55%)	78.09%	78.49%
Aves GenBank	11,880	10,206 (85.91%)	10,206 (85.91%)	74.45%	73.21%
Aves known RefSeq (NP_)	7,204	6,841 (94.96%)	6,841 (94.96%)	77.52%	75.11%
Homo sapiens known RefSeq (NP_)	38,160	31,475 (82.48%)	31,475 (82.48%)	69.26%	63.48%

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

RefSeq

Integrated reference sequences