An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes

Herring, Christopher D; Palsson, Bernhard Ø

doi:10.1186/1471-2164-8-274

BMC Genomics

Table 1 Differences between MG1655 and W3110 Kohara (CGSC # 7167)

From: An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes

Location¹	Gene	b number	Mutation	CGS Detection	Reported as:²	Status³
Small sequence differences
555954	ybcJ	b0528	c>t	yes	SNP	new
556858	folD	b0529	a>t	yes	SNP	new
1092487	ycdT	b1025	c>t	yes	SNP	known
1335418	acnA	b1276	a>g	yes	SNP	known
1650355	intQ	b1579	t>c	yes	SNP	known
2030447	yedJ	b1962	g>a	yes	SNP	known
2865477	rpoS	b2741	g>a	yes	ROI	known
3484227	crp	b3357	c>a	yes	ROI	known
4210321	rrlE	b4009	g>a	undetected		known
4364615	dcuA	b4138	2 nt insertion	yes	ROI	known
IS element insertions
654214	dcuC	b0621	IS5 insertion	yes	ROI	known
1104604	csgC-ymdA	b1043 – 1044	IS2 insertion	undetected		known
1298687	ychE-oppA	b1242 – 1243	IS2 insertion	undetected		known
1463456	ydbA	b1401	IS2 insertion	yes	ROI	new
1976519	flhD-yecG	b1892 – 1895	IS5 insertion	undetected		known
2033459	yedS – hchA	b1966 – 1967	IS5 insertion	yes	ROI – 1 probe	new
2172870	gatA	b2094	IS5 insertion	yes	ROI	known
2315483	rcsC	b2218	IS2 insertion	yes	ROI	known
2404811	lrhA-yfbQ	b2289 – 2290	IS1 insertion	yes	ROI – 1 probe	known
2696426	yfhB	b2560	IS30 insertion	yes	ROI	new
3260500	tdcD	b3115	IS5 insertion	yes	ROI – 1 probe	known
3378961	degQ	b3234	IS2 insertion	yes	ROI	new
3550943	malP-malT	b3417 – 3418	IS5 insertion	yes	ROI	new
3681321	dctA	b3528	IS30 insertion	yes	ROI	new
3886653	tnaA-tnaC	b3707 – 3708	IS5 insertion	yes	ROI – 1 probe	known
3889134	tnaB	b3709	IS5 insertion	yes	ROI	known
3891777	yieE-yidZ	b3711 – 3712	IS2 insertion	yes	ROI	known
4229085	yjbC	b4022	IS2 insertion	yes	ROI	new
4304907	alsK	b4084	IS5 insertion	yes	ROI	known
Deletions/Inversions
1395267 – 1397616	ynaJ-fnr	b1332 – 1334	deletion	yes	ROI	new
~2556721 – 2563354	intZ-yffS	b2442 – 2450	deletion	yes	ROI	known
3424826 – 4207943		b3276 – 4008	Inversion	undetected		known

1. Location is given based on the MG1655 genome (GenBank accession # U00096.2)
2. Detected differences were reported by Nimblegen as Single Nucleotide Polymorphisms (SNPs) or in non-called Regions Of Interest (ROIs). Most differences detected in ROIs were reported by multiple nearby probes, but were reported in only one probe in cases as noted.
3. This column indicates whether the sequence difference is present in the published genome sequence of W3110.

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ISSN: 1471-2164

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