query_snps.gff

query_snps.gff

query_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 query-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 query_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 IGV visualisation of the results output in the query_snps.gff file:

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