BMC Genomics

Table 1 Size and repeat structure of E. coli genomes estimated by icosihenamer (21-mer) analysis

From: Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

	Genome sequence (bp)
	Strain A_03_34		Strain B_04_28		Strain C_04_22		Strain D_04_27		Strain E_01_37		DH1 (reference)
Copy number^a	Unique	Total	Unique	Total	Unique	Total	Unique	Total	Unique	Total	Unique	Total
1×	4,650,095	4,650,095	4,834,774	4,834,774	4,590,007	4,590,007	5,002,844	5,002,844	4,836,194	4,836,194	4,494,886	4,494,886
2×	34,059	68,119	5,364	10,728	177,520	355,041	45,770	91,541	111,882	223,764	14,578	29,196
3×	3,550	10,649	8,511	25,532	25,052	75,156	9,630	28,890	34,198	102,595	6,959	20,877
4×	1,158	4,632	6,296	25,183	8,270	33,079	2,235	8,939	30,549	122,197	2,072	8,288
5×	845	4,223	24	119	5,855	29,277	447	2,236	8,777	43,887	1,874	9,370
6×	0	0	286	1,714	2,271	13,627	196	1,175	4,611	27,665	1,415	8,490
7×	2,208	15,455	1,283	8,982	2,786	19,505	5,489	38,420	8,167	57,168	5,132	35,924
8×	2,566	20,530	3,311	26,486	4,028	32,222	3,170	25,360	3,301	26,405	213	1,704
9×	0	0	41	365	1	13	99	887	662	5,961	23	207
10×	0	0	6	64	424	4,242	6	56	989	9,888	26	260
11 × -20×	107	1669	24	329	679	10,796	1,331	17,155	3,080	45,197	1,240	18,757
21 × -79×	14	333	32	835	709	17,629	70	1,884	68	1,590	62	2,728
Cumulative totals:		4,775,705		4,935,111		5,180,594		5,219,387		5,502,511		4,630,687

^aEach row corresponds to the number of nucleotides and the total amount of genome sequence inferred from the mixed Poisson model fit to each peak of the 21-mer spectrum of short reads for each of the novel E. coli strains (Figure 1A-E), and from direct counts of 21-mer in the E. coli DH1 genome sequence.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com