The BASE COUNT line of the DDBJ flat file format will be changed from DDBJ release 56 (Dec. 2003), corresponding to the relaxation of the maximum sequence length restriction¡Ê350,000 bp/entry¡Ëin the entry that had been practised at DDBJ/EMBL/GenBank International Nucleotide Sequence Databases.
In the BASE COUNT line of the DDBJ flat file format, 6 digits had been allocated for each number of a, c, g, t and other bases in the sequence. Hereafter, in the new flat file format, 9 digits are allocated for each number of a, c, g and t, while the numbers of other bases are removed.
In accordance with the relaxation of sequence length limitation, GenBank had already dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003).
We DDBJ have decided to maintain the BASE COUNT line in our flat file format from the view that GC contents are still important information to characterize the sequence.
Prior to publication of release 56 in December, 2003, the new DDBJ flat file format is adopted to daily data update from Dec. 3.

Following is an example of the new BASE COUNT line. 
    = = = = = = = = example = = = = = = = =    1    6   11   16   21   26   31   36   41   46   51   56   61   66   71    |----|----|----|----|----|----|----|----|----|----|----|----|----|----|    BASE COUNT    123456789 a    123456789 c    123456789 g    123456789 t

For detailed explanation of flat files of DDBJ format, please refer to Guidance for Nucleotide Sequence Data Submission to DDBJ (Guidance 10. Explanation of DDBJ flat file format)
If you have any questions about the change, please send an e-mail to ddbj@ddbj.nig.ac.jp.
Thank you very much for your understanding and cooperation.