Assessing the Quality of Whole Genome Alignments in Bacteria

Table 1

The 41 bacteria pairs. Pair: number of the pair. Organism: names of the organisms. Size: genome size in base pairs. MAGIC: MAGIC's results. Mauve: Mauve's results. Seg.: segmentation size. Ratio: conserved percentage. The pairs are sorted in alphabetical order. For each pair, the best obtained scores are marked in bold.

Pair	Organism	Size	MAGIC		Mauve
			Seg.	Ratio	Seg.	Ratio
1	Anaplasma marginale St. Maries	1197687	74	0.35	94	0.37
	Anaplasma phagocytophilum HZ	1471282
2	Bacillus cereus ATCC 14579	5411809	63	0.77	260	0.77
	Bacillus cereus E33L (zebra killer)	5300915
3	Blochmannia floridanus	705557	1	0.67	1	0.67
	Blochmannia pennsylvanicus	791654
4	Bacteroides fragilis YCH46	5277274	58	0.87	146	0.88
	Bacteroides fragilis NCTC 9343	5205140
5	Bartonella henselae Houston-1	1931047	12	0.73	37	0.74
	Bartonella quintana Toulouse	1581384
6	Bordetella pertussis Tohama I	4086189	147	0.79	189	0.8
	Bordetella bronchiseptica RB50	5339179
7	Buchnera aphidicola APS	640681	1	0.76	2	0.76
	Buchnera aphidicola Sg	641454
8	Campylobacter jejuni subsp. jejuni NCTC 11168	1641481	3	0.9	8	0.9
	Campylobacter jejuni RM1221	1777831
9	Clostridium perfringens 13	3031430	9	0.82	94	0.83
	Clostridium perfringens SM101	2897393
10	Cyanobacteria bacterium Yellowstone A-Prime (Synechococcus sp. JA-3-3Ab)	2932766	330	0.67	561	0.71
	Cyanobacteria bacterium Yellowstone B-Prime (Synechococcus sp. JA-2-3 𝐵^′a(2-13))	3046682
11	Dehalococcoides ethenogenes 195	1469720	20	0.7	47	0.71
	Dehalococcoides sp. CBDB1	1395502
12	Ehrlichia ruminantium Welgevonden (South Africa)	1516355	2	0.96	13	0.96
	Ehrlichia ruminantium Gardel	1499920
13	Francisella tularensis subsp. tularensis SCHU S4	1892819	54	0.96	67	0.96
	Francisella tularensis subsp. holarctica OSU18	1895727
14	Haemophilus influenzae Rd KW20 (serotype d)	1830138	13	0.87	34	0.87
	Haemophilus influenzae 86-028NP (nontypeable)	1913428
15	Helicobacter pylori 26695	1667867	25	0.87	67	0.87
	Helicobacter pylori J99	1643831
16	Listeria monocytogenes EGD-e (serotype 1/2a)	2944528	14	0.79	47	0.79
	Listeria innocua CLIP 11262 (serotype 6a)	3011208
17	Legionella pneumophila Lens	3345687	14	0.86	64	0.86
	Legionella pneumophila Paris	3503610
18	Mycoplasma genitalium G-37	580076	6	0.56	13	0.56
	Mycoplasma pneumoniae M129	816394
19	Mycoplasma hyopneumoniae 232	892758	16	0.94	37	0.94
	Mycoplasma hyopneumoniae 7448	920079
20	Mycobacterium tuberculosis H37Rv, laboratory strain	4411532	3	0.99	10	0.99
	Mycobacterium tuberculosis CDC1551, clinical strain	4403837
21	Neisseria meningitidis MC58 (serogroup B)	2272351	14	0.83	321	0.87
	Neisseria meningitidis Z2491 (serogroup A)	2184406
22	Nitrobacter winogradskyi Nb-255	3402093	109	0.52	301	0.53
	Nitrobacter hamburgensis X14	4406967
23	Psychrobacter arcticum 273-4	2650701	27	0.69	148	0.69
	Psychrobacter cryohalolentis K5	3059876
24	Pseudomonas fluorescens Pf-5	7074893	182	0.54	391	0.55
	Pseudomonas fluorescens PfO-1	6438405
25	Prochlorococcus marinus SS120 (subsp. marinus CCMP1375)	1751080	32	0.46	84	0.48
	Prochlorococcus marinus MIT 9312	1709204
26	Rhodopseudomonas palustris CGA009	5459213	170	0.59	392	0.61
	Rhodopseudomonas palustris HaA2	5331656
27	Rickettsia prowazekii Madrid E	1111523	16	0.69	27	0.7
	Rickettsia felis URRWXCal2	1485148
28	Streptococcus agalactiae 2603 (serotype V)	2160267	12	0.9	20	0.9
	Streptococcus agalactiae A909 (serotype Ia)	2127839
29	Staphylococcus aureus subsp. aureus N315, meticillin-resistant (MRSA)	2814816	13	0.93	83	0.93
	Staphylococcus aureus subsp. aureus MW2	2820462
30	Shigella flexneri 301 (serotype 2a)	4607203	22	0.98	38	0.98
	Shigella flexneri 2457T (serotype 2a)	4599354
31	Staphylococcus haemolyticus JCSC1435	2685015	95	0.49	175	0.51
	Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305	2516575
32	Streptococcus pneumoniae TIGR4	2160842	8	0.92	110	0.92
	Streptococcus pneumoniae R6	2038615
33	Streptococcus pyogenes MGAS8232 (serotype M18)	1895017	23	0.91	130	0.93
	Streptococcus pyogenes SSI-1 (serotype M3)	1894275
34	Streptococcus thermophilus CNRZ1066	1796226	6	0.96	31	0.97
	Streptococcus thermophilus LMG18311	1796846
35	Salmonella enterica serovar Typhi CT18	4809037	4	0.99	8	0.99
	Salmonella enterica serovar Typhi Ty2	4791961
36	Synechococcus sp. WH 8102	2434428	188	0.11	323	0.11
	Synechococcus elongatus PCC6301	2696255
37	Thermus thermophilus HB27	1894877	7	0.92	32	0.93
	Thermus thermophilus HB8	1849742
38	Tropheryma whipplei Twist	927303	2	0.98	37	0.98
	Tropheryma whipplei TW08/27	925938
39	Xanthomonas campestris pv. campestris ATCC 33913	5076188	57	0.68	254	0.68
	Xanthomonas campestris pv. vesicatoria	5178466
40	Xylella fastidiosa 9a5c	2679306	25	0.86	266	0.86
	Xylella fastidiosa Temecula1	2519802
41	Yersinia pestis CO92	4653728	23	0.87	48	0.99
	Yersinia pestis KIM	4600755