NCBI Homo sapiens Annotation Release 108

The RefSeq genome records for Homo sapiens 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
• Alignment of the annotated proteins to a set of high-quality proteins: The number of annotated proteins with hits to a set of high-quality proteins
• 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
• Similarity of current and previous assembly: The similarity of the current and previous assembly
• Similarity of alternate and reference assemblies: The similarity of the alternate assemblies to the reference
• Comparison of the current and previous annotations: What proportion of the genes changed in this annotation

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 Homo sapiens Annotation Release 108

Annotation release ID: 108
Date of Entrez queries for transcripts and proteins: May 5 2016
Date of submission of annotation to the public databases: Jun 6 2016
Software version: 7.0

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
GRCh38.p7	GCF_000001405.33	Genome Reference Consortium	03-21-2016	Reference	25 assembled chromosomes; unplaced scaffolds
CHM1_1.1	GCF_000306695.2	Washington University School of Medicine	06-14-2013	Alternate	23 assembled chromosomes

Gene and feature statistics

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

Feature counts

Feature	GRCh38.p7	GRCh38.p7 Primary Assembly	GRCh38.p7 All Alt Loci	GRCh38.p7 PATCHES	CHM1_1.1
Genes and pseudogenes	54,220	53,958	2,427	590	52,600
protein-coding	20,433	20,345	1,016	242	20,131
non-coding	17,835	17,712	672	144	17,397
pseudogenes	15,952	15,901	739	204	15,072
genes with variants	20,089	20,021	570	132	15,326
placed on multiple assembly-units	2,613	na	671	na	na
mRNAs	109,005	108,675	1,812	409	44,096
fully-supported	108,787	108,491	1,785	402	43,952
with > 5% ab initio	127	111	14	2	87
partial	42	37	228	55	659
with filled gap(s)	0	0	0	0	0
placed on multiple assembly-units	1,848	na	609	na	na
known RefSeq (NM_)	43,092	43,023	1,603	357	42,735
model RefSeq (XM_)	65,913	65,652	209	52	1,361
Other RNAs	45,479	43,735	1,840	287	33,765
fully-supported	43,689	42,355	1,513	283	32,400
with > 5% ab initio	0	0	0	0	0
partial	7	7	40	10	111
with filled gap(s)	0	0	0	0	0
placed on multiple assembly-units	373	na	129	na	na
known RefSeq (NR_)	11,689	11,684	394	73	11,451
model RefSeq (XR_)	32,021	30,692	1,119	210	20,967
CDSs	109,591	109,060	1,971	446	44,475
fully-supported	108,787	108,491	1,785	402	43,952
with > 5% ab initio	169	144	20	5	117
partial	42	37	195	50	315
with major correction(s)	81	70	61	20	521
known RefSeq (NP_)	43,092	43,023	1,601	354	42,734
model RefSeq (XP_)	65,913	65,652	209	52	1,361

Detailed reports

Alignment of the annotated proteins to a set of high-quality proteins

The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 19962 coding genes in the GRCh38.p7 primary assembly, 19521 genes had a protein with an alignment covering 50% or more of the query and 18965 had an alignment covering 95% or more of the query. Out of 19751 coding genes in the CHM1_1.1 assembly, 19343 genes had a protein with an alignment covering 50% or more of the query and 18778 had an alignment covering 95% or more of the query.

Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.

Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.

Query: annotated proteins
Target: UniProtKB/Swiss-Prot curated proteins

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 RepeatMasker only.

Assembly name	Assembly accession	% Masked with RepeatMasker	% Masked with WindowMasker
GRCh38.p7	GCF_000001405.33	49.28%	36.10%
CHM1_1.1	GCF_000306695.2	47.21%	33.97%

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 RNA-Seq reads and reported in the RNA-Seq 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.

	GRCh38.p7 Primary Assembly	CHM1_1.1 Primary Assembly
Number of sequences retrieved from Entrez	55,998	55,998
Number (%) of sequences not aligning	22 (0.04%)	97 (0.17%)
Number (%) of sequences with multiple best alignments (split genes)	4 (0.01%)	5 (0.01%)
Number (%) of sequences with CDS coverage < 95%	11 (0.03%)	255 (0.59%)

RNA-Seq alignments

The following RNA-Seq reads from the Sequence Read Archive were also used for gene prediction:

  Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)  Show alignments statistics, by run (ERR, SRR, DRR)

Protein alignments

Assembly-assembly alignments of current to previous assembly

When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First Pass	Total
GRCh38.p7 (Current) Coverage: 99.54%	GRCh38.p7 (Current) Coverage: 99.99%
GRCh38.p2 (Previous) Coverage: 99.86%	GRCh38.p2 (Previous) Coverage: 99.99%
Percent Identity: 99.99%	Percent Identity: 99.99%

Assembly-assembly alignments of alternate to reference assembly

When multiple assemblies of good quality are available for the organism, the annotation of all is done in coordination. The alternate assemblies are aligned to the reference assembly and the best reciprocal best hits are used to identify corresponding regions, that can then be annotated together.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First Pass	Total
CHM1_1.1 (Alternate) Coverage: 99.61%	CHM1_1.1 (Alternate) Coverage: 99.80%
GRCh38.p7 (Reference) Coverage: 91.71%	GRCh38.p7 (Reference) Coverage: 96.58%
Percent Identity: 99.79%	Percent Identity: 99.75%

Comparison of the current and previous annotations

The annotation produced for this release (108) was compared to the annotation in the previous release (107) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). If the assembly was updated between the two releases, alignments between the current and the previous assembly were used to match the current and previous gene and transcript features in mapped regions.

The table below summarizes the changes in the gene set for each assembly as a percent of the number of genes in the current annotation release, and provides links to the details of the comparison in tabular format and in a Genome Workbench project.

	GRCh38.p7 (Current) to GRCh38.p2 (Previous)	CHM1_1.1 (Current) to CHM1_1.1 (Previous)
Identical	49%	66%
Minor changes	28%	12%
Major changes	11%	10%
New	12%	12%
Deprecated	7%	7%
Other	<1%	<1%
Download the report	tabular, Genome Workbench	tabular, Genome Workbench

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