Table 2.

Comparison of outputs of the predicted active prophages by Prophage Tracer with PHASTER or Prophage Hunter in seven coral-associated bacterial strains^a

		Prophage Tracer
Strain name	Prophage	attL_start	attL_end	attR_start	attR_end	Size	PHASTERb	Prophage Hunterc
Erythrobacter aquimaris SCSIO 43205	Pea1	1888722	1888741	1936851	1936870	48129	Questionable (70):	Active (0.9): 1885416–1903092
							1895962–1915899	Active (0.97): 1888722–1936870
								Active (0.91): 1917844–1948048
Ruegeria conchae SCSIO 43209	Prc1	1373446	1373460	1379997	1380011	6551	-	Inactive (0.12):1362384–1392851
Halomonas meridiana SCSIO 43005	Phm1	292609	292683	333351	333425	40742	Intact (150):	Inactive (0.14): 274307–310741
							293153–331437	Active (0.9): 292613–333425
	Phm2	1064123	1064145	1100156	1100178	36033	Intact (150):	Ambiguous (0.73): 1064268–1100128
							1075299–1101737
	Phm3	2090511	2090576	2139945	2140010	49434	Incomplete (20):	Active (0.93): 2077440–2104589
							2090437–2116834	Active (0.97): 2090511–2140010
								Ambiguous (0.76): 2124591–2138678
Vibrio nigripulchritudo SCSIO 43132 (contig1)	Pvn1	353280	353303	367745	367768	14465	-	Ambiguous (0.77): 350448–374105
Marixanthomonas ophiurae SCSIO 43207	Pmo1	2643352	2643371	2676198	2676217	32846	-	-
Mesoflavibacter sabulilitoris SCSIO 43206	Pms1	2668021	2668042	2679241	2679262	11220	-	Inactive (0.34): 2648530–2674443
Zunongwangia mangrovi SCSIO 43204	Pzm1	1472262	1472314	1512357	1512409	40095	Incomplete (30):	Ambiguous (0.72): 1461300–1484415
							1486303–1511274	Active (0.92): 1469187–1485662
								Active (0.95): 1487346–1517819
								Inactive (0.26): 1510309–1532089

^aFull outputs of these three tools and LUMPY are shown in Supplementary Table S6.

^bOutputs of prophage regions predicted by PHASTER (the scores are in parenthesis and the predicted ends are shown). ‘–’ indicates ‘not detected’.

^cOutputs of prophage regions predicted by Prophage Hunter (the scores are in parenthesis and the predicted ends are shown). ‘–’ indicates ‘not detected’.