Flat File Example

The EMBL flat file format should be used for the submission of annotation data, from targeted assembled/annotated sequences to full annotated genome assemblies.

This page provides an example of the format, and may be used as a basis for preparing flat files for submission. When used for this purpose, please do not change any fields currently filled with ‘XXX’. These represent values which will be generated automatically by the ENA processing pipeline, so anything you enter here will be overwritten. On the other hand, be sure to edit any text enclosed in curly brackets ( ‘{’ and ‘}’ ).

To see the full range of available features and qualifiers, please visit WebFeat. To see any upcoming feature table changes see here.

For a list of third party tools which may help with the creation of your flat file or conversion from another format, please see our page on Third Party Tools.

We have some pre-prepared flat file templates available for use with common submission types available too, please see Entry Upload Templates.

ID   XXX; XXX; {'linear' or 'circular'}; XXX; XXX; XXX; XXX.
XX
AC   XXX;
XX
AC * _{entry_name} (where entry_name=sequence name: e.g. _contig1 or _scaffold1)
XX
PR   Project:PRJEBNNNN;
XX
DE   XXX
XX
RN   [1]
RP   1-2149
RA   XXX;
RT   ;
RL   Submitted {(DD-MMM-YYYY)} to the INSDC.
XX
FH   Key           Location/Qualifiers
FH
FT   source        1..588788
FT                 /organism={"scientific organism name"}
FT                 /mol_type={"in vivo molecule type of sequence"}
XX
SQ   Sequence 588788 BP; 101836 A; 193561 C; 192752 G; 100639 T; 0 other;
     tgcgtactcg aagagacgcg cccagattat ataagggcgt cgtctcgagg ccgacggcgc        60
     gccggcgagt acgcgtgatc cacaacccga agcgaccgtc gggagaccga gggtcgtcga       120
     gggtggatac gttcctgcct tcgtgccggg aaacggccga agggaacgtg gcgacctgcg       180
[sequence truncated]...