Interpreting contig alignments to a reference genome
some additional information to your request.
https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/FamilyPhylogeneticTree/Graph/SRR12707453.MN813694.1.gfa
it contain assembled by reference graph
using ncbi tool saute(skesa) which will be public later.
install bandage app and load this graph
https://rrwick.github.io/Bandage/
picture looks intriguing,I would say , run contain many errors located in one position.
Reason? I don’t really know.