Copy numbers of extrachromosomal prophages

  • a Sequence reads mapping to the phage genome out of a total of ∼1 million per sample.

  • b Sequence reads beginning at precisely the terminus of viral genomic DNA.

  • c Sequence reads that span the predicted 5′ and 3′ ends of the genomes.

  • d The ratio of phage/host genome coverage multiplied by the end-spanning reads:total end reads.