A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Table 3 Re-sequenced genome comparisons sequence differences identified among four re-sequenced genomes and their respective finished sequence

a.			Missing Sequence		Failed assembly of repeat sequence tracts		Paralogous cross identification		Sequencing Discrepancy
Isolate	CDS count	Total number of bases	CDS count	total number of bases	CDS count	number of bases ^§	CDS count	total number of bases ^§	CDS count	Number of bases affected
Z2491	1876	1693839	4 (0.2%)	5408	2 (0.2%)	3039	5 (0.3%)	4737	12 (0.6%)	32
FAM18	1914	1767562	9 (0.5%)	21895	6 (0.3%)	9070	8 (0.4%)	6990	9 (0.5%)	24
G2136	1904	1718346	7 (0.4%)	14484	10 (0.5%)	13125	12 (0.6%)	4974	25 (1.3%)	90
H44/76	1975	1784201	8 (0.4%)	16716	7 (0.4%)	14458	17 (0.9%)	4824	25 (1.3%)	76
b.
Isolate	Loci Present		Loci with identical sequence match		Loci with nucleotide sequence discrepancy		Loci that are present but incomplete
Z2491	1872 (99.8%)		1801 (96.2%)		19 (1.0%)		51 (2.7%)
FAM18	1905 (99.5%)		1775 (93.2%)		23 (1.2%)		107 (5.6%)
G2136	1897 (99.6%)		1757 (92.6%)		47 (2.5%)		93 (4.9%)
H44/76	1967 (99.2%)		1821 (92.6%)		49 (2.5%)		97 (4.9%)

§ For each CDS that had either a failed assembly or paralogous cross-identification error the entire CDS length was counted as affected.
Sequence differences were identified using the BIGSdb Genome Comparator tool. All transposase CDS were removed from the analysis. The Z2491 and FAM18 were originally sequenced and finished using ABI373 and 377 or ABI 3700 methods in 2000 and 2007 respectively, and the H44/76 and G2136 genomes were originally sequenced and finished in 2011 using Roche 454 FLX and capillary-based sequencing.

ISSN: 1471-2164