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. 2018 Sep 3;18:446. doi: 10.1186/s12879-018-3356-6

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© The Author(s). 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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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Fig. 4 — Bioinformatic pipeline to obtain the report of amino acid substitutions. Massive sequencing was performed using 454/GS-Junior (Roche), and MiSeq (Illumina) platforms. Each fasta file was subjected to the eight sequential steps depicted in the irregular pentagons with gray background; steps are explained in the text. The outcome is a report of amino acid substitutions with abundances ≥1% compared with the reference sequence. The report is described in two ways: individual amino acid substitutions present at a given frequency (filled panel at the bottom left), and combined amino acid susbtitutions into haplotypes (each at a given frequency) (filled panel at the bottom right)