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Table 1 A comparison of significant positive associations in the linkage network for E. coli genomes to known co-localisation of mobile AMR genes

From: GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

  1. Co-localisation of AMR genes in MGEs were previously determined by Ingle, et al. [19]. Each pair of significantly associated alleles (denoted by alleles 1 and 2, regardless of their roles in a linear model) is also identifiable in the comparative network shown in Fig. 3. Directionality of associations is omitted in this table, hence each pair of alleles only appears once in the table, although the alleles may mutually associated in linear models. Note that an AMR gene may have multiple alleles (whose names are listed in column Allele_1 or Allele_2) or no allele (denoted by a dash sign in the table) present in a network. Abbreviations: LMM, linear mixed model; PLM, penalised logistic model; IBD: identity by descent. Symbols indicating whether a significant association is identified by either an LMM or a PLM: (), yes; (), no. sd: the distance score, which takes into account the distance consistency, measurability, and the probability of IBD. pIBD: an estimate of the probability that APDs used for calculating the sd are in IBD. This probability does not exist when no APD is available