ref_struct.gff

ref_struct.gff

ref_struct.gff is a GFF3 file that contains information about structural differences and local differences that cause alignment fragmentation. All difference locations are given in reference-based coordinates.

All types of differences can be met in the file. An example of the ref_snps.gff file and a detailed description of the information, provided for each difference type, can be found at the wiki page of a difference.

IGV visualisation of the ref_struct.gff file:

Figure 1: IGV visualisation of the results output in the ref_struct.gff file