Table 1.

An overview of basic sequence information statistics and quality of reads after trimming and filtering. The mixed culture was obtained from the co-culturing of E. coli 4 and K. pneumoniae 5 isolates. Coverage of E. coli isolates was calculated by dividing the number of bp in each read over the number of bp in reference genome (E. coli NCTC 13441). Coverage of K. pneumoniae isolates was calculated by dividing the number of bp reads over the number of bp reads in the K. pneumoniae reference genome (median genome size of all K. pneumoniae isolates in NCBI database). Coverage of mixed culture sample was calculated by dividing the number of bp in mix culture sample over the sum of pb of E. coli NCTC 13441 and median genome size of all K. pneumoniae isolates in NCBI database.

	MinION Long Reads					Illumina Short Reads
	Read Length N50 (bp)	Mean Read Quality (Q)	Number of Reads	Total bp	Coverage (X)	Number of Reads	Total bp	Coverage (X)
E. coli 1	2520	11.4	63,036	92,626,571	17.4	670,985	91,989,902	17.2
E. coli 2	1466	11.3	67,331	88,553,163	16.6	597,154	141,802,031	26.6
E. coli 3	1384	11.5	41,103	39,979,342	7.5	1,786,471	396,985,933	74.4
E. coli 4	5956	9.8	81,317	256,369,935	48.0	1,419,582	353,790,894	66.3
E. coli (mean ± SD)	2832 ± 2147	11 ± 0.8	63,197 ± 16,669	119,382,253 ± 94,404,708	22.4 ± 18	1,118,548 ± 579,915	246,142,190 ± 151,648,580	46.1 ± 28
K. pneumoniae 1	1428	11.3	13,694	25,125,702	4.5	889,410	222,836,627	39.8
K. pneumoniae 2	7302	11.5	199,822	859,067,656	153.5	559,060	131,573,009	23.5
K. pneumoniae 3	4250	11.5	51,624	136,843,964	24.5	744,422	111,911,073	20.0
K. pneumoniae 4	2044	9.9	329,042	375,495,020	67.1	1,302,920	313,973,441	56.1
K. pneumoniae 5	3941	9.3	48,463	64,316,017	11.5	712,218	178,050,866	31.8
K. pneumoniae (mean ± SD)	3793 ± 2302	11 ± 1	128,529 ± 133,041	292,169,672 ± 344,844,995	52.2 ± 62	841,606 ± 283,335	191,669,003 ± 80,759,064	34.2 ± 14
Mixed culture sample	4200	9.8	143,076	387,311,832	35.4	2,131,800	531,841,759	48.7