Table 3.

MEGAnnotator2 report of 10 sequentially processed microbial genomes using short- and long-read technologies

SRA	Sequencing output:	High quality reads:	Sequencing output (long reads):	High quality reads (long reads):	16S rRNA gene identity:	ANI screening:	Genome completeness:	Genome contamination:	Average coverage:	Average coverage (long reads):	Number of contigs:	Genome length:	Number of genes:	Number of rRNA genes:	Number of tRNA genes:
ERR5950940	1000000	973651	73857	42648	Shigella boydii 99.9%	Shigella boydii 98.2%	99.97%	0.75%	75	39	55	6,606,912	6,860	22	97
ERR5951433	559060	514029	198629	60015	Klebsiella pneumoniae 99.9%	Klebsiella pneumoniae 99.0%	100%	1.04%	45	86	4	5,595,850	5,217	25	88
SRR12326962	369346	357819	92666	62330	Salmonella enterica 100%	Salmonella enterica 98.8%	100%	0.78%	32	97	5	5,310,747	5,134	22	92
SRR12811523	1000000	991228	196879	106628	Enterobacter aerogenes 99.9%	Klebsiella aerogenes 95.8%	100%	1.11%	49	99	8	5,567,807	5,281	25	90
SRR12811532	1000000	995953	102851	77655	Citrobacter freundii 100%	Citrobacter portucalensis 94.7%	99.94%	1.86%	48	99	16	5,693,281	5,598	25	86
SRR12811547	1000000	996250	222219	79032	Enterobacter cloacae 100%	Enterobacter cloacae 99.7%	98.92%	1.06%	50	98	19	5,496,621	5,248	25	87
SRR13177364	1000000	962158304	158304	61251	Kocuria varians 100%	n.d.	98.68%	0%	163	120	2	2,848,142	2,432	9	48
SRR13249533	850449	845436	109409	43592	Bacillus oleronius 99.8%	Heyndrickxia oleronia 100%	98.30%	6.27%	76	68	2	5,364,016	5,378	36	145
SRR14087463	1000000	991529	90337	62461	Pseudomonas aeruginosa 100%	Pseudomonas aeruginosa 94.1%	99.60%	0.17%	41	66	14	6,729,107	6,213	12	68
SRR21755520	1000000	944753	137078	25119	Agrobacterium arsenijevicii 98.9%	n.d.	97.26%	3.31%	46	52	4	5,773,279	5,401	15	60