Table 3.

Summary of some stages of intermediate files generated from rMAP

Analysis	Metrics	Description
Assembly	Genome length, average genome length, N50, GC content and sequencing depth	Genome length – an estimate of the draft genome assembly length Average genome length – average read length of genomes N50 – length of smallest contig covering 50 % of genome GC content – guanine–cytosine content of draft genome Depth – no. of times each nucleotide position in the draft genome has a read that aligns to that position
Phylogeny		SNPs are used to infer phylogenetic relationships between samples
Variant calling	SNPs	SNP – a single-nucleotide base change from the reference genome that occurs anywhere within the genome
Antimicrobial resistance profiling	Contig, gene, identity, product	Contig – continuous consensus nucleotide sequences without gaps Gene – antibiotic resistance gene identified within the assembly Identity – percentage representing exact nucleotide matches Product – artefact produced from antibiotic resistance gene
Pangenome analysis	Core genes, soft core genes, shell genes, cloud genes	The genes are compared against each other across samples to predict genome plasticity and to detect how much of the accessory genome has been taken up by organisms over the course of time