deletion appears in the reference and in the mutant

[maculatus]

Hello, I am using snippy 4.6.0. I got a deletion described as 28 base pairs. However, when I did the alignment of the reference with the file snps.consensus.fa, the sequences are the same, showing only the sites in the reference. If I aligned the snps.consesus.subs.fa, all the variations describes in the snps.report.txt are there except the 28 base pairs deletion that it is present. Do I miss something? Deletions are not removed from the snps.consensus.fa and snps.consensus.subs.fa? How can I produce an alignment that shows the region that is deleted? Many thanks!