TABLE 3.

Modified sequence motifs in E. faecalis OG1RF and E. coli BL21(DE3) detected by the SMRT analysis pipeline

Strain	Motifa	Total no. of motifs in genome	No. of modified motifs detected (% of total)b	Mean modification QVc	Mean motif coverage
E. faecalis OG1RF	GCNGCAGCd	377	198 (52.5)	73.6	118×
	GCTGCAANNNNNNNT	100	23 (23)	51.4	120×
	GNGCAGCT	163	26 (16)	58.3	119×
E. coli BL21(DE3)(pET28a)	GATC	37,562	37,555 (99.98)	211.4	135×
E. coli expressing OG1RF_11823e	CCGG	47,782	21,776 (45.57)	55.3	83×
E. coli expressing OG1RF_10790e	None detected

^aThe predicted modified position is underlined.

^bThe percent motif detection was calculated by dividing the number of modified motifs that were detected by the total number of motifs in the genome.

^cMean QV for modified bases in motifs.

^dContains overlapping GCNGC motifs.

^eDam modifications were removed during postprocessing of data.