Table 2.

Details on the types of mis-assemblies and feature characteristics for the results presented in Table 1

		Mis-assembly types				Mis-assembly signatures			Suspicious regions
Species	Len	Ins	Del	Join	Inv	Num	aLen	%Len	Num	aLen	%Len
B. anthracis	5.2	0	0	2	0	1,336	831	21.5	127	5,546	13.6
B. suis	3.4	0	0	7	3	1,047	1,354	42.2	158	7,575	35.6
C. burnetii	2.0	0	0	13	9	1,375	1,106	74.3	124	11,455	69.4
C. caviae	1.4	0	0	11	1	625	320	14.1	50	3,896	13.7
C. jejuni	1.8	1	0	3	1	290	613	10.0	61	1,981	6.8
D. ethenogenes	1.8	0	0	8	4	688	691	26.5	88	4,116	20.2
F. succinogenes	4.0	0	1	19	1	1,670	1,387	57.5	266	7,396	48.8
L. monocytogenes	2.9	0	0	1	0	1,381	873	42.1	201	5,254	36.9
M. capricolum	1.0	3	0	0	0	83	835	6.8	16	3,005	4.7
N. sennetsu	0.9	0	0	0	0	91	512	5.4	13	2,328	3.5
P. intermedia	2.7	0	0	19	2	1,655	727	44.5	201	6,263	46.5
P. syringae	6.4	0	1	43	20	2,841	782	34.4	366	5,725	32.4
S. agalactiae	2.1	0	0	16	5	687	793	25.6	112	4,082	21.5
S. aureus	2.8	1	0	34	6	1,850	740	49.0	227	5,582	45.4
W. pipientis	3.3	0	0	17	14	761	1,206	28.1	132	6,395	25.8
X. oryzae	5.0	1	0	74	76	2,569	1,551	79.0	100	27,771	55.1
Totals	46.8	6	2	267	142	18,949	895	35.1	2242	6773	30.0

Phrap mis-assemblies are grouped into tandem insertion (Ins), tandem collapse (Del), mis-join (Join), and inversion (Inv) events in columns 3-6. Columns 7-9 give the total count (Num), average length (aLen), and total length as a percentage of genome (%Len) for the amosvalidate mis-assembly signatures. Columns 10-12 give the same information, but for amosvalidate suspicious regions.