NCBI Arachis hypogaea Annotation Release 100

The RefSeq genome records for Arachis hypogaea 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 Arachis hypogaea Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jun 25 2018
Date of submission of annotation to the public databases: Jul 20 2018
Software version: 8.1

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
arahy.Tifrunner.gnm1.KYV3GCF_003086295.1International Peanut Genome Initiative05-30-2018Reference21 assembled chromosomes

Gene and feature statistics

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

Feature counts

Featurearahy.Tifrunner.gnm1.KYV3
Genes and pseudogenes help111,051
  protein-coding68,149
  non-coding37,332
  transcribed pseudogenes62
  non-transcribed pseudogenes5,508
  genes with variants19,354
  immunoglobulin/T-cell receptor gene segments0
  other0
mRNAs101,028
  fully-supported83,165
  with > 5% ab initio help16,457
  partial326
  with filled gap(s) help43
  known RefSeq (NM_) help0
  model RefSeq (XM_)101,028
non-coding RNAs help54,608
  fully-supported25,771
  with > 5% ab initio help0
  partial1
  with filled gap(s) help1
  known RefSeq (NR_) help0
  model RefSeq (XR_) help53,393
pseudo transcripts help63
  fully-supported58
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help63
CDSs101,111
  fully-supported83,165
  with > 5% ab initio help16,628
  partial316
  with major correction(s) help207
  known RefSeq (NP_) help0
  model RefSeq (XP_) help101,111

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 Arabidopsis thaliana known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 68066 coding genes, 56223 genes had a protein with an alignment covering 50% or more of the query and 22505 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: Arabidopsis thaliana known RefSeq 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 WindowMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
arahy.Tifrunner.gnm1.KYV3GCF_003086295.13.44%60.98%

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

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

References

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