Table 2. Comparison of the genome annotations generated by PGAP-3.1 with the GenBank annotations of the same genomes (snapshot from February 2016).

Data point	# of genes in GenBank annotation	# of predictions matching annotation in 3′ end	% of annotated genes missed in predictions	# of predictions matching annotation in 5′ and 3′ ends	% of predictions with mismatch in 5′ end	# of hypothetical genes in GenBank annotation
Bacillus subtilis	4185	4044	3.4	3768	6.8	232
Chlamydia trachomatis	892	886	0.7	822	7.2	285
E. coli	4140	4093	1.1	3915	4.3	0
Franciscella tularensis	1602	1589	0.8	1330	16.3	202
Mycobacterium leprae	1605	1599	0.4	1391	13.0	14
Mycobacterium tuberculosis	4018	3954	1.6	3342	15.5	508
Neisseria meningitidis	2063	1958	5.1	1705	12.9	529
Pseudomonas aeruginosa	5571	5531	0.7	5051	8.7	1693
Salmonella enterica	4554	4485	1.5	4031	10.1	10
Yersinia pestis	4083	4031	1.3	3429	14.9	332