Methods:

I assembled the different samples with Flye and obtained for all of them 2 chromosomes. 
I rearranged the assembled and reference genomes making them starting from DNA A using Circlator fixstart.
I then compared the fixed assembly to the fixed reference and extracted the SNPs using MUMMER. 
Mummerplot was used to plot the genomic alignments. 
Finally, I annotate the variations using snpEff on a custom database made by retrieving the info for your reference. 
The samples are named CRG1 to CRG6.

Here are the descriptions of the files:

CRG*.fna -> genome assembly
CRG*.bam -> genome alignment
CRG*.bai -> genome alignment index
GCF_000698325.1_ASM69832v1_genomic_fix.fna, GCF_000698325.1_ASM69832v1_genomic_fix.fna.fai -> reference genome and index
GCF_000698325.1_ASM69832v1_genomic_fix.gff.gz -> reference annotation

anno folder ->
CRG*.ann.vcf.gz -> annotated variants
CRG*.snpEff_summary.html -> HTML reports
CRG*.snpEff_summary.csv -> CSV reports
CRG*.snpEff_summary.genes.txt -> summary of affected genes

pdfs folder ->
CRG*_plot.pdf -> plot with genomic alignments of assembly vs reference. Consider that they are linearized but are actually circular.

You can upload the reference, the bam files and the vcf to IGV for checking.

phastest folder ->
output of the phastest tool for detecting the putative prophage genome. Some pictures in png shows the genomic context.