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. 2014 Sep 4;6(9):2368–2379. doi: 10.1093/gbe/evu192

Table 1.

Summary Statistics and Characteristics of Cg Isolates

Isolate Origin Mapped Reads %Used Reads Read Depth %Ns SNPs Genes
M.1001 Missouri, USA Reference 9.21 12,006
i318 Nigeria 60,957,326 86.6 121× 9.83 9,170 12,004
i113173 Zimbabwe 58,434,572 69.8 120× 14.43 160,983 11,920
i47511 Michigan, USA 52,486,812 72.9 108× 13.9 141,118 11,929
iJAB2 Brazil 11,251,096 40.6 24× 25.24 155,561 11,900
i13649 Alabama, USA 46,081,744 89.7 93× 14.72 82,206 11,968
i63127 Germany 62,416,798 92.9 132× 19.79 115,695 11,925
i51134 Nagano, Japan 14,884,038 43.2 31× 19.53 139,134 11,952

Note.—Origin, region where the isolates were collected; mapped reads, the total number of effectively mapped reads from each isolate to the Cg M.1001 genome; %used reads, percentage of the number of sequenced reads effectively used for the assembly; read depth, the average per-base depth for each genome, taking into account only the unambiguous sites; SNPs, number of single nucleotide polymorphisms identified as compared with the Cg M.1001 reference genome; %Ns, for M.1001, the percentage of ambiguously called bases in the reference genome (non A, T, C, or G). For the sequenced isolates, the percentage of the genome with less than three reads coverage and therefore where SNPs were not called. Genes, number of M.1001 genes present in each isolate, considering a gene as “present” if the sequence contains more than 50% length with unambiguous bases.