ref_snps.gff
ref_snps.gff is a GFF3 file that contains information about small and medium local differences that do not cause alignment fragmentation. All difference locations are given in reference-based coordinates.
The following types of differences can be met in this file:
- simple insertions
- simple deletions
- simple substitution
- gap
- inserted gaps
An example of the ref_snps.gff file and a detailed description of the information, provided for each mentioned difference type, can be found at the wiki page of a difference.
Here we provide only the IGV visualization of the results output in the ref_snps.gff file:
Figure 1: IGV visualisation of the results output in the ref_snps.gff file