Prophage integration was determined if at least 1000 bases of the phage contig were aligned to the bacterial genome with at least 95% identity, and the alignment was localized to one or both ends of the phage contig
Prophage integration was determinedif at least 1000 bases of the phage contig were aligned tothe bacterial genome with at least 95% identity, and the alignmentwas localized to one or both ends of the phage contig