Fig. 1

Illustration of two major characteristics of phage genome sequencing used for terminus prediction: Neighboring coverage ratio (NCR) and read edge frequency. I12 phage was used as an example of the selection process of the NCRs that are considered as potential boundaries of terminal repeats. Each dot represents the logarithmic transformed NCR on given nucleotide position with 100-nucleotide window size. Two horizontal dashed lines show the threshold of 1.8 NCR and reciprocal of 1.8. NCRs that are greater than 1.8 or less than reciprocal of 1.8 are collected in a subset of hits (green dots). Within the subset, hits with at least one window coverage of given NCR is 1.8 times greater than genome coverage are considered as significant hits (blue dots). Finally, the local highest and local lowest of significant hits are considered as potential boundaries of terminal repeats (red dots). a The whole-contig NCR of I12 isolate. b The NCR between nucleotide position 68,500 and 72,000. c Every mapped read has one corresponding coordinate at its 5′ end (5′ read edge position) and one at 3′ end (3′ read edge position). The counts of every read edge position were used as one of the indicators of terminus prediction