We thank Liam Shaw for his letter (1), “Null models for gene enrichment in plasmids,” and appreciate the detailed simulation regarding the enrichment analysis of AMR genes on different types of plasmids, which confirms our original conclusions that conjugative plasmids are enriched in these genes (2). We agree that considering the plasmid size is a good point when using a null model for the enrichment analysis as it tests for a completely neutral accumulation of genes. However, using a completely neutral model for all genes on plasmids does not capture the reality of gene content constraints. Conjugative plasmids contain a much larger portion of …

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回复Shaw：AMR基因携带质粒富集分析的挑战【生物科学】

我们感谢 Liam Shaw 的来信 ( 1 )，“质粒中基因富集的空模型”，并感谢关于 AMR 基因在不同类型质粒上的富集分析的详细模拟，这证实了我们最初的结论，即接合质粒在这些基因 ( 2 )。我们同意在使用空模型进行富集分析时考虑质粒大小是一个好点，因为它测试基因的完全中性积累。然而，对质粒上的所有基因使用完全中性的模型并不能捕捉到基因内容限制的现实。接合质粒包含更多的…