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. 2014 Oct 22;15(1):348. doi: 10.1186/s12859-014-0348-4

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© Katz and Pipas; licensee BioMed Central Ltd. 2014

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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SummonChimera prediction of a Salmonella bacteriophage Integration. (A) These are segments taken from the aligned region of a 5’ and 3’ chimera. Blue is bacterial sequence [NCBI Genome: NC_011294], red is bacteriophage sequence [NCBI Genome:NC_019488], and green is homology to both. The numbers indicate the reference sequence nucleotide position. The ambiguous region (green) is 84 nucleotides long. The blue (host) and red (virus) arrows show the 5’ to 3’ direction of the host and virus reference strands. (B) The number of reads (depth of coverage) at each nucleotide position in the 5’ and 3’ chimeras for host and virus are shown. The ambiguous region of the chimera is counted twice (once for the host and virus positions) due to the unknown nature of where the integration occurs.