Comparison of the microbial genes annotated in GenBank files with the CDSs predicted by the AMIGA strategy
			Number of CDSs				Annotated GNF (% vs OA)					Potential NG (% vs AP)
Species	Length	G+C	OA	AP	CC	(%)	Total	Pc	Status		Pc	Total	Pc	Status
code	(Mb)	(%)					(OA -CC)	<0.2	WRONG	SUSPI	>=0.4	(AP-CC)	>=0.4	NEW	AMBIG
AERPE	1.67	56	2694	1721	1545	(57.3)	42.65	42.24	33.96	4.94	0.00	10.23	8.08	2.56	5.35
AQUAE	1.55	43	1522	1713	1511	(99.3)	0.72	0.72	0.13	0.13	0.00	11.79	10.57	5.02	5.55
ARCFU	2.18	49	2436	2459	2360	(96.9)	3.12	2.67	0.78	0.94	0.04	4.03	2.11	0.85	1.22
BORBU	0.91	29	851	830	797	(93.7)	6.35	5.99	3.06	1.53	0.00	3.98	2.53	0.48	1.81
CAMJE	1.64	31	1647	1620	1617	(98.2)	1.82	1.52	0.55	0.49	0.00	0.19	0.19	0.00	0.19
CHLPN	1.23	41	1074	1065	1024	(95.3)	4.66	4.56	0.09	0.00	0.00	3.85	2.25	0.56	1.60
CHLTR	1.04	41	893	909	870	(97.4)	2.58	2.24	0.34	0.56	0.00	4.29	2.09	0.77	1.21
ECOLI	4.63	51	4289	4100	3959	(92.3)	7.69	7.48	1.42	2.12	0.00	3.44	1.80	0.73	1.02
HAEIN	1.83	38	1737	1765	1721	(99.1)	0.92	0.75	0.40	0.17	0.00	2.49	1.30	0.51	0.79
HELPJ	1.64	39	1482	1493	1447	(97.6)	2.36	2.09	0.13	0.20	0.00	3.08	2.08	0.40	1.54
HELPY	1.66	39	1588	1567	1514	(95.3)	4.66	4.28	1.89	0.44	0.00	3.38	1.91	0.70	1.08
METJA	1.66	31	1723	1766	1705	(99.0)	1.04	0.99	0.12	0.70	0.00	3.45	2.38	0.85	1.53
METTH	1.75	50	1869	1841	1793	(95.9)	4.07	4.01	1.82	1.02	0.00	2.61	1.36	0.16	1.20
MYCGE	0.58	32	483	550	474	(98.1)	1.86	1.86	0.41	0.00	0.00	13.82	8.55	6.00	2.18
MYCPN	0.81	40	688	805	664	(96.5)	3.49	3.34	0.29	0.87	0.00	17.52	11.80	4.60	6.96
MYCTU	4.41	66	3913	4096	3746	(95.7)	4.27	3.71	0.64	1.61	0.08	8.54	3.83	1.32	2.34
NEIMA	2.18	52	2063	1908	1802	(87.3)	12.65	11.63	3.64	1.65	0.00	5.56	2.10	0.63	1.31
NEIMB	2.27	52	2128	1960	1810	(85.1)	14.94	14.47	5.83	2.16	0.00	7.65	4.39	2.55	1.63
PYRAB	1.76	45	1764	1856	1706	(96.7)	3.29	3.29	0.00	0.40	0.00	8.08	4.85	1.45	3.39
PYRHO	1.74	42	2059	1813	1643	(79.8)	20.20	19.86	14.67	1.31	0.00	9.38	5.90	2.76	3.09
RICPR	1.10	29	834	886	818	(98.1)	1.92	1.68	0.72	0.60	0.00	7.67	5.76	2.37	3.39
SYNY3	3.57	48	3163	3111	2965	(93.7)	6.26	6.01	0.03	1.20	0.00	4.69	2.06	0.51	1.51
THEMA	1.86	46	1872	1876	1816	(97.0)	2.99	2.78	1.12	0.85	0.00	3.20	1.39	0.48	0.85
TREPA	1.14	53	1040	1034	964	(92.7)	7.31	6.92	3.56	2.40	0.00	6.77	3.00	0.68	2.03
UREPA	0.75	25	612	608	589	(96.2)	3.76	3.59	0.49	1.14	0.00	3.13	1.97	0.00	1.97
VIBCH	4.03	47	3882	3857	3568	(91.9)	8.09	5.51	2.32	2.01	0.00	7.49	3.37	0.21	3.09
See the publication for details on shaded cells. Abbreviations: CDSs, coding sequences; OA, original annotation; AP, AMIGA prediction; CC, common CDSs to both OA and AP; GNF, gene not found; NG, new gene; Pc, coding average probability of a CDS; SUSPI, suspicious; AMBIG, ambiguous. See Methods for species abbreviations.