Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data

Chung, Cheng-Han; Walter, Michael H.; Yang, Luobin; Chen, Shu-Chuan (Grace); Winston, Vern; Thomas, Michael A.

doi:10.1186/s12864-017-3744-0

Table 2 Summary of terminus prediction on selected isolates in this study and nine published phages

From: Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data

Phage	Sequencer	# reads	Coverage	Contig size	Contig form	^a5′ hit	^b5′ NCR	^c5′ REP	^d5′ REF	^e3′ hit	^f3′ NCR	^g3′ REP	^h3′ REF	5′ terminus flanking sequence	3′ terminus flanking sequence
Novel Phages
SBP8a	Roche/454	38455	87.27	158794	Circular	111794	1.874	111794	117	114616	0.159	114616	238	5′-TCAGGTAGAA	AGAAAAACCT-3′
SBP8a	MiSeq	4662176	4670.87	158822	Circular	29634	1.889	30078	2434	32372	0.526	29983	2455	N/A	N/A
ⁱI13	PGM	186893	345.92	157905	Circular	111600	2.036	111610	110	114359	0.42	114359	274	5′-AAACCGTATG	AGAAAAACCT-3′
I48	MiSeq	2975178	4042.41	157912	Circular	72862	1.819	73296	1332	74149	0.524	73201	1261	N/A	N/A
Q8	PGM	72799	115.53	158180	Circular	156549	68.497	156549	965	no hit	N/A	156836	114	5′-AGGTTTTGTG	N/A
Q11	MiSeq	2411528	15285.66	26005	Linear	no hit	N/A	15118	6717	no hit	N/A	15126	6090	N/A	N/A
Published phage with suggested packaging mechanism
Direct Terminal Repeat
Adelynn	MiSeq	250419	215.43	162356	Circular	18032	3.346	18032	261	20724	0.499	20724	171	5′-GGGTTTTTAT	CCGCCTACCC-3′
Nigalana	Roche/454	35451	98.06	160174	Circular	6458	2.296	6458	121	9324	0.542	9324	95	5′-AGGTTTTTCT	CGTTCTACCT-3′
Troll	PGM	32949	29.17	163019	Circular	no hit	N/A	62795	7	no hit	N/A	43962	9	N/A	N/A
Circular permutation
Breeniome	MiSeq	138039	60.10	154434	Circular	no hit	N/A	26061	17	no hit	N/A	48207	19	N/A	N/A
Teardrop	Roche/454	9807	27.05	155389	Circular	no hit	N/A	10666	26	11109	0.497	11109	28	N/A	CCGCTCCGTT-3′
Zeenon	PGM	203150	179.03	155292	Circular	no hit	N/A	139104	23	no hit	N/A	10008	22	N/A	N/A
3′ overhangs
Equemioh13	MiSeq	150088	394.34	53042	Circular	40880	4.803	40880	276	no hit	N/A	41030	191	5′-TGCGGCCGCC	N/A
Zetzy	Roche/454	9157	80.92	48463	Linear	34529	3.321	34529	116	no hit	N/A	34586	70	5′-CCTGTGCGCC	N/A
Lilith	PGM	215716	668.86	50827	Circular	no hit	N/A	5180	89	no hit	N/A	3846	113	N/A	N/A

The numbers in bold font indicate the significant hits of potential termini
^a5′ hit: nucleotide position of significant NCR hit at 5′ boundary of high coverage region
^b5′ NCR: the ratio of 5′ significant NCR hit
^c5′ REP: 5′ read edge position with highest frequency
^d5′ REF: read edge frequency at 5′ REP
^e3′ hit: nucleotide position of significant NCR hit at 3′ boundary of high coverage region
^f3′ NCR: the ratio of 3′ significant NCR hit
^g3′ REP: 3′ read edge position with highest frequency
^h3′ REF: read edge frequency at 3′ REP
ⁱI13 is one of I48-like isolate

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ISSN: 1471-2164

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