Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary

Table 1 Highest-ranking genes for association with LZD resistance MICs ≥ 128 μg/mL

Gene	Comment	OR	p	Pairwise p	Accession	Reference
cfr	cfr-family 23S ribosomal methyltransferase	18	0.0089	0.0156 - 0.1093	AGJ70604	[33]
pinE	DNA recombinase (pLRSA417-associated)	Inf	0.0038	0.03125 - 0.03125	EXP54287	[34]
cueR	HTH-type transcriptional regulator	Inf	0.0123	0.03125 - 0.03125	AJM87290	[34]
Merged^a	Presumed plasmid genes	Inf	0.0123	0.0625 - 0.0625	-	-
blaR1	Beta-lactamase regulatory protein	0.067	0.0237	0.0625 - 0.3125	WP_001096374	[35]
Hypo.	Hypothetical protein	Inf	0.0350	0.0625 - 0.0625	-	-

P values < = 0.05 in italics
^aYolD-like protein, TrbC/VIRB2-family protein, seven hypothetical proteins
OR odds ratio, p naïve p value, Pairwise p range of p values from the pairwise comparisons, Emp p empirical p value after 1000 permutations

ISSN: 1474-760X