SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs

BMC Genomics

Table 3 Methylation motifs of C. coli BFR-CA-9557

No.	Motif	Modified Position	Modification Type	% Motifs Detected	# of Motifs Detected	# of Motifs in Genome	Mean Modi-fication QV¹	Mean Motif Coverage	Partner Motif
A	RAATTY	3	^m6A	98.67	27795	28170	309.40	235.73	RAATTY
B	GATC	2	^m6A	99.66	7512	7538	344.25	257.15	GATC
C	RCATC	3	^m6A	99.43	4381	4406	274.48	256.54
D	CAAGAA	6	^m6A	99.71	2069	2075	290.35	249.45
E	GGGTDA	6	^m6A	99.44	1607	1616	327.70	254.15
F	DACATTGB	4	^m6A	69.69	223	320	80.60	255.05
G1	TAAANNNNNGTG	3	^m6A	99.75	392	393	271.96	259.91	CACNNNNNTTTA
G2	CACNNNNNTTTA	2	^m6A	99.75	392	393	331.81	263.02	TAAANNNNNGTG
H1	CAAYNNNNNNNTTYG	3	^m6A	99.58	237	238	316.89	246.49	CRAANNNNNNNRTTG
H2	CRAANNNNNNNRTTG	4	^m6A	99.58	237	238	276.97	247.15	CAAYNNNNNNNTTYG

¹ QV = quality value
Methylation motifs were identified using the PacBio SMRT Analysis software (see Methods). Column 2 shows the sequence consensus of the motif, whereby non-uniform positions are represented by IUPAC ambiguity codes. Column 3 and 4 denote the position of the modified base within the motif and the type of methylation. Column 5 represents the fraction of a motif’s occurrences in the genome (column 7) for which a methylation has been detected (column 6). Column 8 and 9 denote the average modification quality (in Phred Q-scores) and average coverage of motifs detected as modified. The last column shows the partner motif, i.e. the reverse complement of the motif

ISSN: 1471-2164