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README for ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS  

Created: December 15, 2011
Updated: February 15, 2012
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National Center for Biotechnology Information (NCBI)
National Library of Medicine
National Institutes of Health
8600 Rockville Pike
Bethesda, MD 20894, USA
tel: (301) 496-2475
fax: (301) 480-9241
email: info@ncbi.nlm.nih.gov (for general questions)
email: genomes@ncbi.nlm.nih.gov (for specific questions)

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This FTP directory distributes data presented in the NCBI Genome 
database available at:
   http://www.ncbi.nlm.nih.gov/genome/

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NOTICE:
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This FTP area 
   - ftp://ftp.ncbi.nlm.nih.gov/genomes/genomeprj/
has been discontinued on November 15, 2012

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Directory Content:
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This directory contains summary reports conveying the organism scope and 
detailed genome project reports grouped by major taxonomic divisions.

The taxonomic division reports include information on genome data submitted 
to the primary archival sequence data that is exchanged among members of the 
International Nucleotide Sequence Database Collaboration (INSDC) and genome 
data represented in NCBI RefSeq dataset. 

These files correspond to the tables available online at: 
http://www.ncbi.nlm.nih.gov/genome/browse/


File Name              File Content
--------------------------------------------------------------

overview.txt:   Comprehensive report of organisms that have 
               one or many genome sequencing projects that 
               may be complete, in progress or planned.

eukaryotes.txt: Eukaryotic genome sequencing projects 
               excluding projects that represent only organelles.

prokaryotes.txt: Prokaryotic genome sequencing projects                                      
                excluding projects that represent only plasmids
                               
viruses.txt:   Viral genome sequencing projects 
               This report includes only data represented in 
               the RefSeq dataset. 

prok_reference_genomes.txt: List of reference genome: small curated subset of 
                                         really good and scientifically important prokaryotic genomes (see detail description below).
                                         
prok_representative_genomes.txt:  List of all selected representative prokaryotic genomes (see detail description below).

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Update frequency:
       4 first files are updated daily
        Reference and representative files are updated manually
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File formats and column description:
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All taxonomy terms are defined by the NCBI Taxonomy database.

The first line of each file begins with â€#’ and provides column 
header names and not data.

The following file definitions are formatted as:
  
Column Name | Description

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overview.txt file:
------------------
Organism/Name  Organism name at the species level according 
Kingdom        Taxonomic division: Archaea, Bacteria, Eukaryota, or Viruses 
Group                  Commonly used organism groups 
                       Eukaryota: Animals, Fungi, Plants, Protists;                           
                       Prokaryota: group corresponds to phylum; 
                       Viruses: groups defined as the first level (not ranked)                        
                       below the kingdom of Viruses

SubGroup       NCBI Taxonomy level below group:
                       Eukaryota: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians
                       Reptiles, Roundworms, Ascomycetes, Basidiomycetes, 
                       Land Plants, Green Algae, Apicomplexans, Kinetoplasts; 
                       Prokaryota: sub-groups correspond to class level; 
                       Viruses: sub-groups correspond to families including floating genera 

Size (Mb)      Estimated genome size 
Chrs           Number of chromosomes 
Organelles     Number of the organelles 
Plasmids       Number of plasmids 
BioProjects    Number of genome sequencing projects 

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eukaryotes.txt:
---------------
#Organism/Name Organism name at the species level    
BioProject     BioProject Accession number (from BioProject database)
Group          Commonly used organism groups: 
                        Animals, Fungi, Plants, Protists;
SubGroup       NCBI Taxonomy level below group: 
                       Mammals, Birds, Fishes, Flatworms, Insects, Amphibians
                       Reptiles, Roundworms, Ascomycetes, Basidiomycetes, 
                       Land Plants, Green Algae, Apicomplexans, Kinetoplasts; 
Size (Mb)      Total length of DNA submitted for the project 
GC%            Percent of nitrogenous bases (guanine or cytosine) in 
               DNA submitted for the project
Assembly       Name of the genome assembly (from NCBI Assembly database)
Chromosomes    Number of chromosomes submitted for the project       
Organelles     Number of organelles submitted for the project 
Plasmids       Number of plasmids submitted for the project 
WGS            Four-letter Accession prefix followed by version as                  
               defined in WGS division of GenBank/INSDC
Scaffolds      Number of scaffolds in the assembly
Genes          Number of Genes annotated in the assembly
Proteins       Number of Proteins annotated in the assembly  
Release Date   First public sequence release for the project
Modify Date    Sequence modification date for the project
Status         Highest level of assembly:
                       Chromosomes  one or more chromosomes are assembled
                       Scaffolds or contigs  sequence assembled but no chromosomes
                       SRA or Traces  raw sequence data available 
                       No data  no data is connected to the BioProject ID

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prokaryotes.txt:
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Organism/Name          Organism name usually at the species level 
BioProject             BioProject Accession number (from BioProject database)
Group                  Phylum 
SubGroup               Class level 
Size (Mb)              Total length of DNA submitted for the project
GC%                    Percent of nitrogenous bases (guanine or cytosine) in 
                       DNA submitted for the project 
Chromosomes/RefSeq     Refseq chromosome sequence accessions 
Chromosomes/INSDC      GenBank chromosome sequence accessions 
Plasmids/RefSeq        Refseq plasmid sequence accessions
Plasmids/INSDC         GenBank plasmid sequence accessions   
WGS                    Four-letter Accession prefix followed by version as                  
                       defined in WGS division of GenBank/INSDC
Scaffolds              Number of scaffolds in the assembly
Genes                  Number of Genes annotated in the assembly
Proteins               Number of Proteins annotated in the assembly  
        
Release Date           First public sequence release for the project
Modify Date            Sequence modification date for the project
Status                 Highest level of assembly: 
                               Chromosomes  chromosome is represented by gapless contig
                               Scaffolds or contigs  sequence assembled but no chromosomes
                               SRA or Traces  raw sequence data available 
                               No data  no data is connected to the BioProject ID

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viruses.txt:
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Organism/Name  Organism name usually at the species level 
BioProject     BioProject Accession number (from BioProject database)
                       Note: Only Refseq projects are reported; 
                       INSDC Viral genomes are primarily out of scope for BioProject
Group          Group is defined as the first level (not ranked)                            
               below the kingdom of Viruses
SubGroup       Sub-groups correspond to families including floating genera 
Size (Kb)      Total length of nucleotide sequence
GC%            Percent of nitrogenous bases (guanine or cytosine) in 
                DNA submitted for the project 
Host           Natural host of a virus
Segmemts       Number of segments in viral genome
Genes          Number of Genes annotated in viral genome
Proteins       Number of Proteins annotated in viral genome
Release Date   First public sequence release for the project
Modify Date    Sequence modification date for the project    
Status         Complete - only complete viral genomes are considered


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prok_reference_genomes.txt:
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Species/genus   Species name (or genus for some genomes having Entrez Genome record on 
                genus level)
Genomes         Number of genomes for this species (or genus)
Organism name   Name of organism (can be strain name)
Chromosomes     Refseq and INSDC Chromosome accessions
Plasmids        Refseq and INSDC plasmid accessions (only 1st one, with "..."if more 
                than 1 plasmid in genome
CODE            Code (abbreviated source code, explained below)
Comment         Comment 
Pubmed          Pubmed IDs  
Link            Link to external resource

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prok_representative_genomes.txt:
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Species/genus   Species name (or genus for some genomes having Entrez Genome record on 
                genus level)
Genomes         Number of genomes for this species (or genus)
Organism name   Name of organism (can be strain name)
Chromosomes     Refseq and INSDC Chromosome accessions
Plasmids        Refseq and INSDC plasmid accessions (only 1st one, with "..."if more 
                than 1 plasmid in genome
CODE            Code (abbreviated source code, explained below)
Comment         Comment 
Pubmed          Pubmed IDs  
Link            Link to external resource

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Archaea and Bacteria reference and representative genomes
Code definitions:

    CLI = Clinical Isolate
    TYS = Type Strain
    FGS = First Genome sequenced
    PRT = Proteomics
    UPR = UniProt genomes
    QfO = species selected by the "Quest For Orthologs" group
    PHY = representative member at a phylogenetically interesting position 
    MOD = Model organism
    CCA = Community Consortium Annotation
    CALC= Calculated
    COM = Community selected reference
    

Each species in Entrez genome collection that has assembly data, either complete or WGS, 
has at least one reference or representative genome. For some well-studied species of great 
biomedical interest or high diversity more than one reference or representative is selected.

Reference genomes are defined as genomes of high quality sequence and annotation and/or 
the isolates that have been used by the research community for clinical studies, 
experimental validation, comparative analysis.

The source of reference genomes:

    UniProt reference proteome
    The genomes with extensive proteomics support for the annotation.
    Community curated annotation
    Community selected reference

Representative genomes are selected based on the following rules:

    the only genome sequenced
    the only complete genome for species
    multiple complete genomes or no complete genome
        Type strain
        First complete genome sequenced
        Human Microbiome reference
        Highest assembly quality

Calculated:
For large clades (> 5 genomes) a representative is calculated by protein cluster analysis: 
the genome with maximum number proteins in clusters is selected.