NCBI Homo sapiens Annotation Release 109

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 109

Annotation release ID: 109
Date of Entrez queries for transcripts and proteins: Feb 13 2018
Date of submission of annotation to the public databases: Mar 26 2018
Software version: 8.0


The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
GRCh38.p12GCF_000001405.38Genome Reference Consortium12-21-2017Reference25 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Primary Assembly
All Alt Loci
Genes and pseudogenes help54,64454,2742,4221,315
  transcribed pseudogenes1,0851,0758957
  non-transcribed pseudogenes15,06715,010641358
  genes with variants20,11020,012598329
  immunoglobulin/T-cell receptor gene segments39638716122
  placed on multiple assembly-units help3,227na674na
  with > 5% ab initio help11599115
  with filled gap(s) help0000
  placed on multiple assembly-units help2,480na628na
  known RefSeq (NM_) help50,06549,9871,710963
  model RefSeq (XM_)63,55563,237177141
non-coding RNAs help46,85444,9651,796670
  with > 5% ab initio help0000
  with filled gap(s) help0000
  placed on multiple assembly-units help582na173na
  known RefSeq (NR_) help14,31614,310471240
  model RefSeq (XR_) help30,73329,2961,025412
pseudo transcripts help1,3461,32510964
  with > 5% ab initio help0000
  with filled gap(s) help0000
  placed on multiple assembly-units helpnananana
  known RefSeq (NR_) help1,2321,22410060
  model RefSeq (XR_) help11410194
  with > 5% ab initio help157133168
  with major correction(s) help82776448
  known RefSeq (NP_) help50,06549,9871,708948
  model RefSeq (XP_) help63,56863,237177141

Detailed reports

The counts below do not include pseudogenes.

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 20070 coding genes, 19639 genes had a protein with an alignment covering 50% or more of the query and 19086 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

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.

Primary Assembly
Number of sequences retrieved from Entrez65,648
Number (%) of sequences not aligning26 (0.04%)
Number (%) of sequences with multiple best alignments (split genes)1 (0.00%)
Number (%) of sequences with CDS coverage < 95% help12 (0.02%)

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)