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. 2017 May;27(5):865–874. doi: 10.1101/gr.207456.116

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© 2017 Li et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 1. — Comparison of SNP calling between the assembly-versus-assembly method and resequencing approaches based on read mapping. The Venn diagram with colors corresponding to the bar chart shows the sharing of identified SNPs among the assembly-versus-assembly method and two resequencing algorithms as implemented in SAMtools and GATK. An average of 4.25 M SNPs per breed were specifically identified by the assembly-versus-assembly method (marked as yellow), while only 0.24 k SNPs per breed were categorized by resequencing approaches (marked as red). A significant fraction of the detected SNPs by SAMtools (8.11 M per individual) and GATK (7.77 M per individual) was coincident (7.41 M; or 91.24% of SAMtools and 95.34% of GATK) (Supplemental Fig. S8).