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NCBI Malus sylvestris Annotation Release 100

The RefSeq genome records for Malus sylvestris 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 Malus sylvestris Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Aug 17 2022
Date of submission of annotation to the public databases: Aug 25 2022
Software version: 10.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
drMalSylv7.2GCF_916048215.2WELLCOME SANGER INSTITUTE02-09-2022Reference19 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeaturedrMalSylv7.2
Genes and pseudogenes help53,019
  protein-coding37,480
  non-coding9,851
  Transcribed pseudogenes0
  Non-transcribed pseudogenes5,688
  genes with variants12,473
  Immunoglobulin/T-cell receptor gene segments0
  other0
mRNAs59,440
  fully-supported55,874
  with > 5% ab initio help2,865
  partial155
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)59,440
non-coding RNAs help18,919
  fully-supported16,193
  with > 5% ab initio help0
  partial2
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help18,242
pseudo transcripts help0
  fully-supported0
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help0
CDSs59,561
  fully-supported55,874
  with > 5% ab initio help2,976
  partial155
  with major correction(s) help181
  known RefSeq (NP_) help0
  model RefSeq (XP_) help59,561

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 eudicots_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 Arabidopsis thaliana known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 37359 coding genes, 32982 genes had a protein with an alignment covering 50% or more of the query and 15038 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 (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
drMalSylv7.2GCF_916048215.240.27%

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 Nucleotide, Entrez Protein, and SRA, and aligned to the genome.

Transcript alignments

The alignments of the following transcripts with Splign were used for gene prediction:

RNA-Seq alignments

The alignments of the following RNA-Seq reads with STAR were also used for gene prediction:

  Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)
  Show alignments statistics, by run (ERR, SRR, DRR)

SRA Long Read Alignment Statistics

The alignments of the following long RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive with minimap2 were used for gene prediction:

Protein alignments

The alignments of the following proteins with ProSplign were used for gene prediction:

References