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:

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 nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
GRCh38.p7GCF_000001405.33Genome Reference Consortium03-21-2016Reference25 assembled chromosomes; unplaced scaffolds
CHM1_1.1GCF_000306695.2Washington University School of Medicine06-14-2013Alternate23 assembled chromosomes

Gene and feature statistics

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

Feature counts

FeatureGRCh38.p7GRCh38.p7
Primary Assembly
GRCh38.p7
All Alt Loci
GRCh38.p7
PATCHES
CHM1_1.1
Genes and pseudogenes help54,22053,9582,42759052,600
  protein-coding20,43320,3451,01624220,131
  non-coding17,83517,71267214417,397
  pseudogenes15,95215,90173920415,072
  genes with variants20,08920,02157013215,326
  placed on multiple assembly-units help2,613na671nana
mRNAs109,005108,6751,81240944,096
  fully-supported108,787108,4911,78540243,952
  with > 5% ab initio help12711114287
  partial423722855659
  with filled gap(s) help00000
  placed on multiple assembly-units help1,848na609nana
  known RefSeq (NM_) help43,09243,0231,60335742,735
  model RefSeq (XM_)65,91365,652209521,361
Other RNAs help45,47943,7351,84028733,765
  fully-supported43,68942,3551,51328332,400
  with > 5% ab initio help00000
  partial774010111
  with filled gap(s) help00000
  placed on multiple assembly-units help373na129nana
  known RefSeq (NR_) help11,68911,6843947311,451
  model RefSeq (XR_) help32,02130,6921,11921020,967
CDSs109,591109,0601,97144644,475
  fully-supported108,787108,4911,78540243,952
  with > 5% ab initio help169144205117
  partial423719550315
  with major correction(s) help81706120521
  known RefSeq (NP_) help43,09243,0231,60135442,734
  model RefSeq (XP_) help65,91365,652209521,361

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 nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
GRCh38.p7GCF_000001405.3349.28%36.10%
CHM1_1.1GCF_000306695.247.21%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 Entrez55,99855,998
Number (%) of sequences not aligning22 (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% help11 (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)