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NCBI Homo sapiens Annotation Release 110

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 110

Annotation release ID: 110
Date of Entrez queries for transcripts and proteins: Feb 25 2022
Date of submission of annotation to the public databases: Apr 6 2022
Software version: 9.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
GRCh38.p14GCF_000001405.40Genome Reference Consortium02-03-2022Reference25 assembled chromosomes; unplaced scaffolds
T2T-CHM13v2.0GCF_009914755.1T2T Consortium01-24-2022Alternate24 assembled chromosomes

Gene and feature statistics

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

Feature counts

FeatureGRCh38.p14GRCh38.p14
Primary Assembly
GRCh38.p14
All Alt Loci
GRCh38.p14
PATCHES
T2T-CHM13v2.0
Genes and pseudogenes help59,26558,6542,4872,86357,771
  protein-coding20,02419,8538451,06920,011
  non-coding21,89421,57571886120,716
  Transcribed pseudogenes1,2221,2191011481,195
  Non-transcribed pseudogenes15,65415,54765575015,394
  genes with variants20,17120,00161871617,259
  Immunoglobulin/T-cell receptor gene segments40039016224387
  other717061168
  placed on multiple assembly-units help4,425na677nana
mRNAs130,164129,6642,2232,62764,937
  fully-supported127,308126,8342,2092,61564,791
  with > 5% ab initio help1,1191,10496103
  partial3544306304211
  with filled gap(s) help00000
  placed on multiple assembly-units help4,111na778nana
  known RefSeq (NM_) help63,78463,6852,0482,40163,586
  model RefSeq (XM_)66,38065,9791752261,351
non-coding RNAs help47,90645,4181,8321,64443,723
  fully-supported44,82643,0241,4721,49840,722
  with > 5% ab initio help00000
  partial99705851
  with filled gap(s) help00000
  placed on multiple assembly-units help962na202nana
  known RefSeq (NR_) help17,43717,42758759117,372
  model RefSeq (XR_) help28,47426,59991096524,869
pseudo transcripts help1,7411,7021261921,684
  fully-supported1,7201,6871231891,666
  with > 5% ab initio help00000
  partial0014109
  with filled gap(s) help00000
  placed on multiple assembly-units helpnanananana
  known RefSeq (NR_) help1,5841,5751211671,532
  model RefSeq (XR_) help157127525152
CDSs130,755130,0552,3832,63165,325
  fully-supported127,308126,8342,2092,61564,791
  with > 5% ab initio help1,8681,847129132
  partial517354383272430
  with major correction(s) help446541100347
  known RefSeq (NP_) help63,78463,6852,0442,38263,586
  model RefSeq (XP_) help66,39365,9791752261,351

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.1.4 was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the primates_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation.

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 19853 coding genes, 19524 genes had a protein with an alignment covering 50% or more of the query and 19142 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 (if calculated), for each assembly. RepeatMasker results are only calculated for organisms with complete Dfam HMM model collections.

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.p14GCF_000001405.4050.18%36.12%
CHM13 T2T v2.0GCF_009914755.154.96%40.27%

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, minimap2, or ProSplign and passed to Gnomon, NCBI's gene prediction software.

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.p14
Primary Assembly
CHM13 T2T v2.0
Primary Assembly
Number of sequences retrieved from Entrez82,86282,862
Number (%) of sequences not aligning25 (0.03%)52 (0.06%)
Number (%) of sequences with multiple best alignments (split genes)0 (0.00%)0 (0.00%)
Number (%) of sequences with CDS coverage < 95% help15 (0.02%)92 (0.14%)

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)