Table 1.

Description of Pharokka output files

Output files	Description of file contents
.gff	Gff3 feature file with all genomic annotations
.gbk	GenBank formatted feature file
.faa	FASTA file of predicted CDS (amino acid)
.ffn	FASTA file of predicted CDS (nucleotide)
minced_spacers.txt and minced.gff	MinCED CRISPR spacers and parsed CRISPR annotations
aragorn.txt and aragorn.gff	Aragorn tmRNA annotations
trnascan_out.gff	tRNAscan-SE 2 tRNA annotations
cds_functions.tsv	Functional summary counts of CDS
cds_final_merged_output.tsv	Combined output from PHROGs, VFDB and CARD
length_gc_cds_density.tsv	Summary of genome length, GC percentage, coding density
.tbl	Feature table for NCBI (BankIt) submission
top_hits_card.tsv and top_hits_vfdb.tsv	Top hits from CARD and VFDB annotations. Will contain no rows if there are no hits
terL.faa and terL.ffn	Predicted terminase large subunit sequences