Table 5.

Under-represented and over-represented 5-mers of the E. coli data

Group	Template reads				Complement reads				2D reads
	Kmer	Occurrence/100 bp		Diff	Kmer	Occurrence/100 bp		Diff	Kmer	Occurrence/100 bp		Diff
		in Ref	in Templ			in Ref	in Compl			in Ref	in 2D
Under-represented	AAAAA	0.247	0.086	−0.161	CGCCA	0.288	0.092	−0.196	TTTTT	0.251	0.047	−0.204
	TTTTT	0.251	0.093	−0.158	AAAAA	0.247	0.055	−0.192	AAAAA	0.247	0.058	−0.189
	CGCTG	0.258	0.104	−0.155	TTTTT	0.251	0.065	−0.186	CAAAA	0.170	0.111	−0.058
	GCTGG	0.279	0.148	−0.132	CACCA	0.184	0.054	−0.130	AAAAT	0.195	0.138	−0.057
	CGCCA	0.288	0.168	−0.120	CCAGC	0.288	0.162	−0.126	AAAAG	0.132	0.081	−0.051
	CCAGC	0.288	0.180	−0.108	CGCTG	0.258	0.135	−0.123	CGCCA	0.288	0.239	−0.049
	GCCAG	0.280	0.173	−0.107	GCCAG	0.280	0.157	−0.122	TAAAA	0.145	0.097	−0.048
	CTGGC	0.278	0.178	−0.100	CAGCA	0.262	0.140	−0.122	TGGTG	0.185	0.138	−0.048
	CAGCA	0.262	0.168	−0.095	CTGGC	0.278	0.159	−0.119	CGCTG	0.258	0.213	−0.046
	CGGCA	0.222	0.129	−0.093	TGGCG	0.275	0.163	−0.112	GCCAG	0.280	0.238	−0.042
Over-represented	ACCCC	0.040	0.136	0.096	ACCCC	0.040	0.143	0.103	CAAAT	0.105	0.164	0.059
	CCCCG	0.055	0.149	0.093	CCCCG	0.055	0.134	0.079	GGGGT	0.039	0.074	0.035
	CCCCC	0.033	0.122	0.089	CCCCA	0.064	0.128	0.065	CCCAA	0.047	0.080	0.033
	CCCCA	0.064	0.138	0.075	CCTAG	0.003	0.066	0.063	TGAAT	0.121	0.154	0.033
	CCTAG	0.003	0.075	0.072	CTGAG	0.050	0.112	0.063	GAAGG	0.094	0.127	0.033
	GCCCC	0.062	0.131	0.069	TACCC	0.073	0.136	0.062	CGGGG	0.054	0.087	0.032
	CTCCC	0.039	0.107	0.067	CCTAA	0.026	0.087	0.061	ACCGT	0.123	0.155	0.032
	TCTAC	0.048	0.113	0.065	GACCC	0.040	0.100	0.060	CGTGA	0.102	0.134	0.032
	TCCCC	0.056	0.121	0.065	TCCCC	0.056	0.115	0.059	GAAGC	0.124	0.156	0.032
	TACCC	0.073	0.138	0.064	TCCTA	0.013	0.071	0.058	AGGCA	0.093	0.124	0.031

Note: Poretools was used to extract FASTA sequences for template, complement, and 2D reads from the FAST5 files. The 5-mer counts of the reads of the E. coli data [13] and of the reference assembly were calculated separately using the oligonucleotide frequency function of the R package Biostring. Frequencies of each 5-mer occurrence in reads per 100 bp were calculated and differences in reads relative to Ref are indicated. Ref, reference assembly; Templ, template read; Compl, complement read.