Table 2.

Mutations detected in L. plantarum ATCC14917 following passage under selection pressure from gentamicin and following subsequent passage in the absence of gentamicin, i.e., when selection pressure was removed.

Subculture medium	Chromosome	Region/Site	Type		Variant Length(bp)	Variant ratio	Gene or Locus-tag	Product	Amino acid change	KEGG Orthology
LSM with gentamicin (under selection pressure)	GL379762	355182-355204	SV	Deletion	23	1	lmrB	Drug resistance MFS transporter	TGIIIPLT	K18926
		355240-355249			10				DVVM
	GL379763	280882-280909	SV	Deletion	28	0.68	HMPREF0531_10299	Transcriptional regulator, AraC family	LSSSPNCSSE	K18325
		281102-281123			22				VVVGDNPM
		281269-281302			34				IDYQREMTVGLLMTEL
		281402-281406			5				FTY
		281522-281530			9				LFNK
	GL379765	297964-297981	Insertion		1	0.57	HMPREF0531_11866	Hypothetical protein	multiple changes	NA
	GL379766	260916	SNP		1	NA	HMPREF0531_12271	Hypothetical protein	p.Ile38Leu	NA
LSM without gentamicin (selection pressure removed)	GL379765	297964-297981	Insertion		1	0.57	HMPREF0531_11866	Hypothetical protein	multiple changes	NA
	GL379766	260916	SNP		1	NA	HMPREF0531_12271	Hypothetical protein	p.Ile38Leu	NA

SNP: single nucleotide polymorphism. SV: structural variant. Variant length: the number of nucleotide replacement, deletion, or insertion. Variant ratio: This fraction is intended to give a hint toward the zygosity of the InDel. The closer the value to 1, the higher the likelihood that the variant is homozygous. Amino acid change: amino acid(s) replacement or deletion; one insertion introduced in the gene results in multiple changes of amino acids thereafter. NA: not applicable.