High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

Table 1 Clipped read analysis enables locating coordinates of inducible prophages in gut bacterial genomes

Strain	Phage	Start site prophage	End site prophage
A. muciniphila YL44	YL44 phage 1	969482	1008291
A. muciniphila YL44	YL44 phage 2	2566025	2602918
B. coccoides YL58	YL58 phage 1	128601	174693
E. coli HS	E. coli HS phage 1	916812	948289
A. muris KB18	KB18 phage 1	2602856	2642096
F. plautii YL31	YL31 phage 1	1009760	1046747
F. plautii YL31	YL31 phage 2	2984604	3026727

Reads originating from circularised or concatenated viral genomes align only partially to the reference genome generating clipped reads. The accumulation of clipped reads at the attL and attR sites allows for identifying the exact start and end coordinates of inducible prophages

ISSN: 2049-2618