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NCBI Lucilia cuprina Annotation Release 101

The RefSeq genome records for Lucilia cuprina 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 Lucilia cuprina Annotation Release 101

Annotation release ID: 101
Date of Entrez queries for transcripts and proteins: Feb 23 2022
Date of submission of annotation to the public databases: Mar 3 2022
Software version: 9.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM2204524v1GCF_022045245.1North Carolina State University02-08-2022Reference6 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureASM2204524v1
Genes and pseudogenes help15,856
  protein-coding13,927
  non-coding1,784
  Transcribed pseudogenes5
  Non-transcribed pseudogenes139
  genes with variants3,522
  Immunoglobulin/T-cell receptor gene segments0
  other1
mRNAs22,082
  fully-supported20,294
  with > 5% ab initio help922
  partial377
  with filled gap(s) help4
  known RefSeq (NM_) help6
  model RefSeq (XM_)22,076
non-coding RNAs help2,446
  fully-supported1,714
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help1,825
pseudo transcripts help5
  fully-supported4
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help5
CDSs22,082
  fully-supported20,294
  with > 5% ab initio help1,000
  partial377
  with major correction(s) help134
  known RefSeq (NP_) help6
  model RefSeq (XP_) help22,076

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 diptera_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 Drosophila melanogaster known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 13927 coding genes, 12265 genes had a protein with an alignment covering 50% or more of the query and 5486 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 (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 WindowMasker only.
Assembly nameAssembly accession% Masked with WindowMasker
ASM2204524v1GCF_022045245.154.29%

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

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
JAKMAP01 (Current) Coverage: 69.89%JAKMAP01 (Current) Coverage: 71.76%
Lcup_2.0 (Previous) Coverage: 76.31%Lcup_2.0 (Previous) Coverage: 76.86%
Percent Identity: 93.57%Percent Identity: 93.54%

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.

ASM2204524v1 (Current) to Lcup_2.0 (Previous)
Identical help5%
Minor changes help55%
Major changes help22%
New help17%
Deprecated help25%
Other help1%
Download the reporttabular, Genome Workbench

References