NCBI Arachis ipaensis Annotation Release 101

The RefSeq genome records for Arachis ipaensis 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 ipaensis Annotation Release 101

Annotation release ID: 101
Date of Entrez queries for transcripts and proteins: May 2 2017
Date of submission of annotation to the public databases: May 13 2017
Software version: 7.4

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Araip1.1GCF_000816755.2Iowa State University04-25-2017Reference10 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureAraip1.1
Genes and pseudogenes help49,814
  protein-coding37,716
  non-coding9,775
  pseudogenes2,323
  genes with variants11,428
mRNAs57,621
  fully-supported46,852
  with > 5% ab initio help9,385
  partial2,317
  with filled gap(s) help2,019
  known RefSeq (NM_) help0
  model RefSeq (XM_)57,621
Other RNAs help21,380
  fully-supported20,817
  with > 5% ab initio help0
  partial25
  with filled gap(s) help25
  known RefSeq (NR_) help0
  model RefSeq (XR_) help20,818
CDSs57,621
  fully-supported46,852
  with > 5% ab initio help9,605
  partial1,912
  with major correction(s) help1,335
  known RefSeq (NP_) help0
  model RefSeq (XP_) help57,621

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 Arabidopsis thaliana known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 37716 coding genes, 29652 genes had a protein with an alignment covering 50% or more of the query and 11505 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
Araip1.1GCF_000816755.23.11%52.21%

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

Assembly-assembly alignments of current to previous assembly

When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.

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
Araip1.1 (Current) Coverage: 100.00%Araip1.1 (Current) Coverage: 100.00%
Araip1.0 (Previous) Coverage: 100.00%Araip1.0 (Previous) Coverage: 100.00%
Percent Identity: 100.00%Percent Identity: 100.00%

Comparison of the current and previous annotations

The annotation produced for this release (101) was compared to the annotation in the previous release (100) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). If the assembly was updated between the two releases, alignments between the current and the previous assembly were used to match the current and previous gene and transcript features in mapped regions.

The table below summarizes the changes in the gene set for each assembly as a percent of the number of genes in the current annotation release, and provides links to the details of the comparison in tabular format and in a Genome Workbench project.

Araip1.1 (Current) to Araip1.0 (Previous)
Identical help16%
Minor changes help50%
Major changes help14%
New help20%
Deprecated help9%
Other help<1%
Download the reporttabular, Genome Workbench

References

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