Table 4.

Results of filtering treatments for strain Towne varL

Filtering treatment	k	Reads after filtering (no.)	Contig size (kb)			Contigs (no.)			Velvet parameter (value)*
			Median	Maximum	Total	All	>1 kb	>5 kb	Exp_cov	Cov_cutoff
Unfiltered	21	5079235	8	25	246	237	36	16	290	42
	25	5079235	14	44	246	178	30	13	250	41
Singletons removed	21	1682785	13	32	231	65	27	14	210	82
Overall quality:
>1900	21	2338321	3	16	292	765	64	16	110	11
>1700	21	4156964	7	32	264	383	46	13	220	26
	25	4156964	11	32	243	150	32	16	190	44
Quality truncation, length >29	21	2609325	7	15	242	233	36	13	65	26
Truncated to length:
40	21	5079235	14	45	251	256	21	12	190	25
	25	5079235	18	44	242	114	23	12	160	38
35	21	5079235	29	65	246	176	18	8	150	26
	25	5079235	31	68	242	99	13	10	110	30
30	21	5079235	24	68	240	90	20	11	105	32
	25	5079235	54	68	237	61	8	7	60	24

*Each dataset was assembled using Velvet-0.7.31 (see Methods). Exp_cov, Optimal expected coverage; cov_cutoff, optimal coverage cut-off.