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

Table 3 Comparison of terminal position between the prediction from NGS data and identification from primer walking method

Terminus predicted by NGS data					Terminus identified by primer walking sequencing
Name	Sequencer	Contig size	^a5′ ter.	^b3′ ter.	5′ ter.	^cdistance	5′ terminus flanking sequence	3′ ter.	distance	3′ terminus flanking sequence	length of DTR
SBP8a	Roche/454	158794	111794	114616	111796	+2	5′-AGGTAGAACG	114616	0	AGAAAAACCT-3′	2821
^dI13	PGM	157905	111610	114359	111537	−73	5′- AGGTAGAACG	114359	0	AGAAAAACCT-3′	2823
^dI22	PGM	157889	106421	109166	106348	−73	5′- AGGTAGAACG	109169	+3	AGAAAAACCT-3′	2822
Q8	PGM	158180	156549	^g5025	156549	0	5′- AGGTTTTGTG	5099	+74	GGGTCTACCC-3′	6731
^eQ10	PGM	158174	86402	^g93056	86402	0	5′- AGGTTTTGTG	93130	+74	GGGTCTACCC-3′	6729
Q11	MiSeq	26005	N/A	N/A	^h-9	N/A	5′ AAAATGTAAA	^h + 43	N/A	ATATACATTT-3′	N/A
^fI46	MiSeq	24896	N/A	N/A	^h-740	N/A	5′ AAAATGTAAA	^h + 421	N/A	ATATACATTT-3′	N/A

^a5′ ter.: nucleotide coordinate of 5′ terminus
^b3′ ter.: nucleotide coordinate of 3′ terminus
^cdistance: position difference to prediction
^dI13 and I22 are I48-like isolates
^eQ10 is one of Q8-like isolate
^fI46 is one of Q11-like isolate
^gLocation of Q8-like stain physical ends was assisted by designing primers from several hundred bases upstream of the common predicted hits
^hThe position outside of contig sequence was calculated by the relative position of coordinates of contig sequence from NGS data. Minus coordinate represents 5′ upstream of first bp of contig; Plus coordinate represents 3′ downstream of last bp of contig

ISSN: 1471-2164