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NCBI Microplitis demolitor Annotation Release 101

The RefSeq genome records for Microplitis demolitor 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 Microplitis demolitor Annotation Release 101

Annotation release ID: 101
Date of Entrez queries for transcripts and proteins: Oct 16 2015
Date of submission of annotation to the public databases: Oct 19 2015
Software version: 6.4

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Mdem2GCF_000572035.2University of Illinois at Urbana-Champaign10-07-2015Referenceunplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureMdem2
Genes and pseudogenes help12,755
  protein-coding12,144
  non-coding526
  pseudogenes85
  genes with variants3,284
mRNAs18,586
  fully-supported16,219
  with > 5% ab initio help1,470
  partial805
  with filled gap(s) help533
  known RefSeq (NM_) help0
  model RefSeq (XM_)18,586
Other RNAs help1,011
  fully-supported826
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help828
CDSs18,586
  fully-supported16,219
  with > 5% ab initio help1,535
  partial555
  with major correction(s) help95
  known RefSeq (NP_) help0
  model RefSeq (XP_) help18,586

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 Drosophila melanogaster known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 12144 coding genes, 8648 genes had a protein with an alignment covering 50% or more of the query and 2683 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: Drosophila melanogaster 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
Mdem2GCF_000572035.25.09%39.76%

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

No transcript evidence was used in this annotation.

Short read transcript alignments

The following short reads (RNA-Seq) 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
Mdem2 (Current) Coverage: 89.47%Mdem2 (Current) Coverage: 91.50%
Mdem1 (Previous) Coverage: 82.04%Mdem1 (Previous) Coverage: 83.86%
Percent Identity: 99.78%Percent Identity: 99.76%

References