NCBI Homo sapiens Annotation Release 105

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 105

Annotation release ID: 105
Date of Entrez queries for transcripts and proteins: Aug 3 2013
Date of submission of annotation to the public databases: Aug 13 2013
Software version: 5.1


The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
GRCh37.p13GCF_000001405.25Genome Reference Consortium06-28-2013Reference25 assembled chromosomes; unplaced scaffolds
CHM1_1.1GCF_000306695.2Washington University School of Medicine06-14-2013Alternate23 assembled chromosomes
CRA_TCAGchr7v2GCF_000002135.2The Centre for Applied Genomics09-01-2004Alternate1 assembled chromosomes
HuRefGCF_000002125.1J. Craig Venter Institute09-24-2007Alternate24 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 help40,15839,9474282,47139,0092,10638,070
  genes with variants15,06814,9941407478,7184188,620
  placed on multiple assembly-units help2,665na349nananana
  with > 5% ab initio help20318102216211180
  placed on multiple assembly-units help2,171na293nananana
  known RefSeq (NM_) help34,63234,6063401,85734,3671,60234,212
  model RefSeq (XM_)32,88530,1281,0201,73777543631
  model RefSeq (XM_) with correction help17150221015
Other RNAs help15,06314,15144375411,40857610,854
  with > 5% ab initio help0000000
  placed on multiple assembly-units help279na60nananana
  known RefSeq (NR_) help6,6236,618803046,4582836,328
  model RefSeq (XR_) help7,0116,5381193543,9462423,650
  with > 5% ab initio help22019702317512192
  known RefSeq (NP_) help34,63234,6053401,84634,3651,60234,185
  model RefSeq (XP_) help32,88530,1281,0201,73777543631
  model RefSeq (XP_) with correction help17150221015

Detailed reports

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 short reads and reported in the Short read transcript 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
Primary Assembly
Primary Assembly
Primary Assembly
Number of sequences retrieved from Entrez42,33942,33942,33942,339
Number (%) of sequences not aligning20 (0.05%)60 (0.14%)39,716 (94.39%)253 (0.60%)
Number (%) of sequences with multiple best alignments (split genes)30 (0.07%)26 (0.06%)1 (0.05%)326 (0.78%)
Number (%) of sequences with CDS coverage < 95% help65 (0.19%)234 (0.68%)6 (0.37%)1,981 (5.77%)

Short read transcript alignments

The following short reads (RNA-Seq) from the Short Read Archive were also used for gene prediction:

  Hide alignments statistics

Protein alignments

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 PassTotal
CHM1_1.1 (Alternate) Coverage: 99.68%CHM1_1.1 (Alternate) Coverage: 99.90%
GRCh37.p13 (Reference) Coverage: 94.22%GRCh37.p13 (Reference) Coverage: 98.73%
Percent Identity: 99.89%Percent Identity: 99.86%
First PassTotal
CRA_TCAGchr7v2 (Alternate) Coverage: 99.75%CRA_TCAGchr7v2 (Alternate) Coverage: 99.92%
GRCh37.p13 (Reference) Coverage: 5.18%GRCh37.p13 (Reference) Coverage: 5.50%
Percent Identity: 99.94%Percent Identity: 99.91%
First PassTotal
HuRef (Alternate) Coverage: 99.04%HuRef (Alternate) Coverage: 99.45%
GRCh37.p13 (Reference) Coverage: 93.01%GRCh37.p13 (Reference) Coverage: 97.88%
Percent Identity: 99.87%Percent Identity: 99.80%


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