Exported Gap.fasta file
In the NextGENe viewer, the File > Export > Gap.fasta file option is available only for very small projects (reference less than 10Mbp). A .fasta file is created which shows the region of the reference file to which each read is aligned. The file lists the following information:
• The entire reference sequence.
• Each aligned read, beginning with the first aligned read.
• The read name is shown in the header line. The sequence lines include "*" , "-", "_" or ".") to indicate empty base positions of the reference, followed by the sequence of the read. For example, a read that aligns to the 2nd base of the reference is shown as "*ACTG. “