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

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

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%)   
  1. § For each CDS that had either a failed assembly or paralogous cross-identification error the entire CDS length was counted as affected.
  2. 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.