Table 1. The genetic repertoire of prophages in Data Set 1 and Data Set 2.

	Number of prophages containing a gene of this type
Gene	Count in Data Set 1			Count in Data Set 2
	Intact	Questionable	Incomplete	Intact	Questionable	Incomplete
terminase	317	25	14	292	53	58
portal	277	9	3	283	67	48
head	299	16	25	281	79	86
injection	14	0	2	4	0	0
tail	413	46	86	419	116	141
protease	82	3	5	72	12	22
transposase	195	32	75	190	173	144
integrase	346	54	85	312	94	165
lysis	226	19	11	52	6	6
plate	121	5	0	143	20	28
capsid	225	14	18	233	50	40
lysin	235	17	19	165	32	22
flippase	2	0	20	0	1	4
Total	2752	240	363	2446	603	764