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. 2017 Aug 9;18:594. doi: 10.1186/s12864-017-3980-3

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© The Author(s). 2017

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. 2 — The number of variants called in the 14 sugarcane germplasm accessions. a Venn diagram showing overlapping SNPs among five genome reference-based callers, Tassel, Stacks, Samtools, GATK, and Freebayes. b Percentage of specific SNPs and concordant SNPs of the total SNPs called by five genome reference-based callers, Tassel, Stacks, Samtools, GATK, and Freebayes. c Venn diagram showing overlapping short insertions or deletions (InDels) among three reference-based callers, Samtools, GATK, and Freebayes